From 37c7d7960ec29c5e13ff25d84acb98f167b5ffd2 Mon Sep 17 00:00:00 2001 From: "Brian P. Walenz" Date: Mon, 17 Oct 2016 15:16:31 -0400 Subject: [PATCH] Fix gcc6 C++11 warnings. Issue #270. --- src/AS_RUN/fragmentDepth.C | 4 +- src/AS_UTL/AS_UTL_fileIO.C | 14 +- src/AS_UTL/AS_UTL_stackTrace.C | 2 +- src/AS_UTL/bitPackedArray.C | 4 +- src/AS_UTL/bitPackedArray.H | 20 +-- src/AS_UTL/bitPackedFile.C | 10 +- src/AS_UTL/bitPackedFile.H | 2 +- src/AS_UTL/kMer.C | 4 +- src/AS_UTL/kMerHuge.H | 10 +- src/AS_UTL/memoryMappedFile.H | 4 +- src/AS_UTL/readBuffer.C | 6 +- src/AS_UTL/stddev.H | 2 +- src/AS_UTL/sweatShop.C | 14 +- src/AS_global.C | 2 +- src/AS_global.H | 55 +++--- src/bogart/AS_BAT_AssemblyGraph.C | 28 +-- src/bogart/AS_BAT_BestOverlapGraph.C | 24 +-- src/bogart/AS_BAT_Instrumentation.C | 162 +++++++++--------- src/bogart/AS_BAT_Logging.C | 2 +- src/bogart/AS_BAT_MarkRepeatReads.C | 2 +- src/bogart/AS_BAT_OverlapCache.C | 90 +++++----- src/bogart/AS_BAT_PopBubbles.C | 8 +- src/bogart/AS_BAT_PromoteToSingleton.C | 2 +- src/bogart/AS_BAT_ReadInfo.C | 2 +- src/bogart/AS_BAT_ReadInfo.H | 6 +- src/bogart/AS_BAT_SplitDiscontinuous.C | 10 +- src/bogart/AS_BAT_TigVector.C | 8 +- src/bogart/AS_BAT_Unitig.C | 8 +- src/bogart/addReadsToUnitigs.C | 2 +- src/bogart/analyzeBest.C | 2 +- src/bogart/buildGraph.C | 2 +- src/bogus/bogus.C | 12 +- src/correction/filterCorrectionOverlaps.C | 30 ++-- src/correction/generateCorrectionLayouts.C | 6 +- src/erateEstimate/erateEstimate.C | 16 +- src/falcon_sense/createFalconSenseInputs.C | 2 +- src/falcon_sense/outputFalcon.C | 4 +- src/fastq-utilities/fastqAnalyze.C | 18 +- src/fastq-utilities/fastqSample.C | 26 +-- src/fastq-utilities/fastqSimulate-sort.C | 4 +- src/fastq-utilities/fastqSimulate.C | 10 +- src/merTrim/merTrim.C | 26 +-- src/merTrim/merTrimResult.H | 4 +- src/mercy/mercy-regions.C | 30 ++-- src/mercy/mercy.C | 28 +-- src/meryl/estimate-mer-threshold.C | 26 +-- src/meryl/leaff-blocks.C | 6 +- src/meryl/leaff-duplicates.C | 10 +- src/meryl/leaff-gc.C | 2 +- src/meryl/leaff-partition.C | 10 +- src/meryl/leaff-statistics.C | 18 +- src/meryl/leaff.C | 8 +- src/meryl/libleaff/fastaFile.C | 14 +- src/meryl/libleaff/fastaStdin.C | 2 +- src/meryl/libleaff/fastqFile.C | 16 +- src/meryl/libleaff/fastqStdin.C | 4 +- src/meryl/libleaff/seqCache.C | 4 +- src/meryl/libleaff/seqStore.C | 20 +-- src/meryl/libleaff/seqStream.C | 20 +-- src/meryl/libmeryl.C | 22 +-- src/meryl/meryl-args.C | 2 +- src/meryl/meryl-binaryOp.C | 4 +- src/meryl/meryl-build.C | 76 ++++---- src/meryl/meryl-dump.C | 26 +-- src/meryl/meryl-estimate.C | 6 +- src/meryl/meryl-merge.C | 2 +- src/meryl/simple.C | 8 +- .../splitReads-subReads.C | 2 +- src/overlapBasedTrimming/splitReads.C | 56 +++--- .../trimReads-largestCovered.C | 8 +- src/overlapBasedTrimming/trimReads-quality.C | 4 +- src/overlapBasedTrimming/trimReads.C | 28 +-- src/overlapErrorAdjustment/analyzeAlignment.C | 24 +-- .../correctOverlaps-Correct_Frags.C | 12 +- .../correctOverlaps-Read_Olaps.C | 6 +- .../correctOverlaps-Redo_Olaps.C | 20 +-- src/overlapErrorAdjustment/correctOverlaps.C | 4 +- src/overlapErrorAdjustment/correctOverlaps.H | 2 +- .../findErrors-Read_Frags.C | 4 +- .../findErrors-Read_Olaps.C | 2 +- src/overlapErrorAdjustment/findErrors.C | 16 +- .../overlapInCore-Build_Hash_Index.C | 32 ++-- .../overlapInCore-Find_Overlaps.C | 6 +- .../overlapInCore-Process_Overlaps.C | 4 +- src/overlapInCore/overlapInCore.C | 58 +++---- src/overlapInCore/overlapInCorePartition.C | 28 +-- src/overlapInCore/overlapReadCache.C | 2 +- src/stores/gatekeeperCreate.C | 40 ++--- src/stores/gatekeeperDumpFASTQ.C | 10 +- src/stores/gatekeeperDumpMetaData.C | 10 +- src/stores/gkStore.C | 34 ++-- src/stores/gkStore.H | 22 +-- src/stores/ovOverlap.C | 10 +- src/stores/ovStore.C | 86 +++++----- src/stores/ovStore.H | 2 +- src/stores/ovStoreBucketizer.C | 6 +- src/stores/ovStoreBuild.C | 48 +++--- src/stores/ovStoreDump.C | 2 +- src/stores/ovStoreFile.C | 4 +- src/stores/ovStoreIndexer.C | 8 +- src/stores/ovStoreSorter.C | 18 +- src/stores/ovStoreStats.C | 24 +-- src/stores/tgStore.C | 6 +- src/stores/tgStoreCompress.C | 8 +- src/stores/tgStoreCoverageStat.C | 4 +- src/stores/tgStoreDump.C | 12 +- src/stores/tgStoreFilter.C | 16 +- src/stores/tgTig.C | 18 +- src/stores/tgTigSizeAnalysis.C | 9 +- src/utgcns/libNDalign/NDalign.C | 2 +- src/utgcns/libcns/unitigConsensus.C | 6 +- src/utgcns/stashContains.C | 2 +- src/utgcns/stashContains.H | 4 +- src/utgcns/utgcns.C | 12 +- 114 files changed, 881 insertions(+), 893 deletions(-) diff --git a/src/AS_RUN/fragmentDepth.C b/src/AS_RUN/fragmentDepth.C index 3e0375e89..af490f123 100644 --- a/src/AS_RUN/fragmentDepth.C +++ b/src/AS_RUN/fragmentDepth.C @@ -99,7 +99,7 @@ computeStuff(uint32 *V, uint32 N, } if (histogramBig) { - fprintf(stderr, "histogramBig: "F_U32"\n", histogramBig); + fprintf(stderr, "histogramBig: " F_U32 "\n", histogramBig); exit(1); } @@ -197,7 +197,7 @@ void outputResult(AS_IID lastiid, if (E > N) { E = N; } computeStuff(V, N, i, E, &mode, &mean, &median); - fprintf(stdout, "%s\t"F_U32"\t"F_U32"\t"F_U32"\t%f\t"F_U32"\n", lastiid, i, E, mode, mean, median); + fprintf(stdout, "%s\t" F_U32 "\t" F_U32 "\t" F_U32 "\t%f\t" F_U32 "\n", lastiid, i, E, mode, mean, median); } safe_free(V); } diff --git a/src/AS_UTL/AS_UTL_fileIO.C b/src/AS_UTL/AS_UTL_fileIO.C index f07ffa728..084a1b84e 100644 --- a/src/AS_UTL/AS_UTL_fileIO.C +++ b/src/AS_UTL/AS_UTL_fileIO.C @@ -76,7 +76,7 @@ AS_UTL_safeWrite(FILE *file, const void *buffer, const char *desc, size_t size, if (errno) { fprintf(stderr, "safeWrite()-- Write failure on %s: %s\n", desc, strerror(errno)); - fprintf(stderr, "safeWrite()-- Wanted to write "F_SIZE_T" objects (size="F_SIZE_T"), wrote "F_SIZE_T".\n", + fprintf(stderr, "safeWrite()-- Wanted to write " F_SIZE_T " objects (size=" F_SIZE_T "), wrote " F_SIZE_T ".\n", towrite, size, written); assert(errno == 0); } @@ -92,7 +92,7 @@ AS_UTL_safeWrite(FILE *file, const void *buffer, const char *desc, size_t size, #ifdef VERIFY_WRITE_POSITIONS if ((expectedposition > 0) && (AS_UTL_ftell(file) != expectedposition)) { - fprintf(stderr, "safeWrite()-- EXPECTED "F_OFF_T", ended up at "F_OFF_T"\n", + fprintf(stderr, "safeWrite()-- EXPECTED " F_OFF_T ", ended up at " F_OFF_T "\n", expectedposition, AS_UTL_ftell(file)); assert(AS_UTL_ftell(file) == expectedposition); } @@ -121,7 +121,7 @@ AS_UTL_safeRead(FILE *file, void *buffer, const char *desc, size_t size, size_t if ((errno) && (errno != EINTR)) { fprintf(stderr, "safeRead()-- Read failure on %s: %s.\n", desc, strerror(errno)); - fprintf(stderr, "safeRead()-- Wanted to read "F_SIZE_T" objects (size="F_SIZE_T"), read "F_SIZE_T".\n", + fprintf(stderr, "safeRead()-- Wanted to read " F_SIZE_T " objects (size=" F_SIZE_T "), read " F_SIZE_T ".\n", toread, size, written); assert(errno == 0); } @@ -130,7 +130,7 @@ AS_UTL_safeRead(FILE *file, void *buffer, const char *desc, size_t size, size_t finish: // Just annoys developers. Stop it. //if (position != nobj) - // fprintf(stderr, "AS_UTL_safeRead()-- Short read; wanted "F_SIZE_T" objects, read "F_SIZE_T" instead.\n", + // fprintf(stderr, "AS_UTL_safeRead()-- Short read; wanted " F_SIZE_T " objects, read " F_SIZE_T " instead.\n", // nobj, position); return(position); } @@ -291,7 +291,7 @@ AS_UTL_sizeOfFile(const char *path) { sprintf(cmd, "gzip -l %s", path); F = popen(cmd, "r"); fscanf(F, " %*s %*s %*s %*s "); - fscanf(F, " %*d "F_OFF_T" %*s %*s ", &size); + fscanf(F, " %*d " F_OFF_T " %*s %*s ", &size); pclose(F); } else if (strcasecmp(path+strlen(path)-4, ".bz2") == 0) { size = s.st_size * 14 / 10; @@ -345,7 +345,7 @@ AS_UTL_fseek(FILE *stream, off_t offset, int whence) { if ((whence == SEEK_SET) && (beginpos == offset)) { #ifdef DEBUG_SEEK // This isn't terribly informative, and adds a lot of clutter. - //fprintf(stderr, "AS_UTL_fseek()-- seek to "F_OFF_T" (whence=%d); already there\n", offset, whence); + //fprintf(stderr, "AS_UTL_fseek()-- seek to " F_OFF_T " (whence=%d); already there\n", offset, whence); #endif return; } @@ -357,7 +357,7 @@ AS_UTL_fseek(FILE *stream, off_t offset, int whence) { } #ifdef DEBUG_SEEK - fprintf(stderr, "AS_UTL_fseek()-- seek to "F_OFF_T" (requested "F_OFF_T", whence=%d) from "F_OFF_T"\n", + fprintf(stderr, "AS_UTL_fseek()-- seek to " F_OFF_T " (requested " F_OFF_T ", whence=%d) from " F_OFF_T "\n", AS_UTL_ftell(stream), offset, whence, beginpos); #endif diff --git a/src/AS_UTL/AS_UTL_stackTrace.C b/src/AS_UTL/AS_UTL_stackTrace.C index 0c55da45d..53852b7d7 100644 --- a/src/AS_UTL/AS_UTL_stackTrace.C +++ b/src/AS_UTL/AS_UTL_stackTrace.C @@ -82,7 +82,7 @@ AS_UTL_envokeGDB(void) { // Child - sprintf(cmd, "gdb -quiet -silent -p "F_U64" -batch -x commands", pid); + sprintf(cmd, "gdb -quiet -silent -p " F_U64 " -batch -x commands", pid); system(cmd); exit(0); #endif diff --git a/src/AS_UTL/bitPackedArray.C b/src/AS_UTL/bitPackedArray.C index 686950b99..c758ab880 100644 --- a/src/AS_UTL/bitPackedArray.C +++ b/src/AS_UTL/bitPackedArray.C @@ -66,7 +66,7 @@ bitPackedArray::get(uint64 idx) { uint64 p = _valueWidth * (idx % _valuesPerSegment); if (idx >= _nextElement) { - fprintf(stderr, "bitPackedArray::get()-- element index "F_U64" is out of range, only "F_U64" elements.\n", + fprintf(stderr, "bitPackedArray::get()-- element index " F_U64 " is out of range, only " F_U64 " elements.\n", idx, _nextElement-1); return(0xdeadbeefdeadbeefULL); } @@ -80,7 +80,7 @@ bitPackedArray::set(uint64 idx, uint64 val) { uint64 s = idx / _valuesPerSegment; uint64 p = _valueWidth * (idx % _valuesPerSegment); - //fprintf(stderr, "s="F_U64" p="F_U64" segments="F_U64"/"F_U64"\n", s, p, _numSegments, _maxSegments); + //fprintf(stderr, "s=" F_U64 " p=" F_U64 " segments=" F_U64 "/" F_U64 "\n", s, p, _numSegments, _maxSegments); if (idx >= _nextElement) _nextElement = idx+1; diff --git a/src/AS_UTL/bitPackedArray.H b/src/AS_UTL/bitPackedArray.H index d7590c74a..654822e58 100644 --- a/src/AS_UTL/bitPackedArray.H +++ b/src/AS_UTL/bitPackedArray.H @@ -164,20 +164,20 @@ public: } #ifdef DEBUG_BPH_GET - fprintf(stderr, "test c="F_U64" and p="F_U64" lastVal="F_U64"\n", + fprintf(stderr, "test c=" F_U64 " and p=" F_U64 " lastVal=" F_U64 "\n", cidx, pidx, _lastVal); - fprintf(stderr, "test c="F_U64"="F_U64"\n", + fprintf(stderr, "test c=" F_U64 "=" F_U64 "\n", cidx, cval); - fprintf(stderr, "test p="F_U64"="F_U64"\n", + fprintf(stderr, "test p=" F_U64 "=" F_U64 "\n", pidx, pval); - fprintf(stderr, "test c="F_U64"="F_U64" and p="F_U64"="F_U64"\n", + fprintf(stderr, "test c=" F_U64 "=" F_U64 " and p=" F_U64 "=" F_U64 "\n", cidx, cval, pidx, pval); #endif if (cval < pval) { #ifdef DEBUG_BPH_GET - fprintf(stderr, "swap c="F_U64"="F_U64" and p="F_U64"="F_U64"\n", + fprintf(stderr, "swap c=" F_U64 "=" F_U64 " and p=" F_U64 "=" F_U64 "\n", cidx, cval, pidx, pval); #endif @@ -204,7 +204,7 @@ public: bool more = false; #ifdef DEBUG_BPH_ADD - fprintf(stderr, "add c="F_U64"="F_U64" -- lastVal="F_U64"\n", + fprintf(stderr, "add c=" F_U64 "=" F_U64 " -- lastVal=" F_U64 "\n", cidx, cval, _lastVal); #endif @@ -217,20 +217,20 @@ public: pidx = (cidx-1) / 2; #ifdef DEBUG_BPH_ADD - fprintf(stderr, "more c="F_U64" and p="F_U64"\n", cidx, pidx); + fprintf(stderr, "more c=" F_U64 " and p=" F_U64 "\n", cidx, pidx); #endif pval = _array->get(pidx); #ifdef DEBUG_BPH_ADD - fprintf(stderr, "test c="F_U64"="F_U64" and p="F_U64"="F_U64"\n", + fprintf(stderr, "test c=" F_U64 "=" F_U64 " and p=" F_U64 "=" F_U64 "\n", cidx, cval, pidx, pval); #endif if (pval > cval) { #ifdef DEBUG_BPH_ADD - fprintf(stderr, "swap c="F_U64"="F_U64" and p="F_U64"="F_U64"\n", + fprintf(stderr, "swap c=" F_U64 "=" F_U64 " and p=" F_U64 "=" F_U64 "\n", cidx, cval, pidx, pval); #endif @@ -254,7 +254,7 @@ public: void dump(void) { for (uint32 i=0; i<_lastVal; i++) - fprintf(stderr, "HEAP["F_U32"]="F_U64"\n", i, _array->get(i)); + fprintf(stderr, "HEAP[" F_U32 "]=" F_U64 "\n", i, _array->get(i)); } void clear(void) { diff --git a/src/AS_UTL/bitPackedFile.C b/src/AS_UTL/bitPackedFile.C index cdd85c59f..102af9dbd 100644 --- a/src/AS_UTL/bitPackedFile.C +++ b/src/AS_UTL/bitPackedFile.C @@ -213,7 +213,7 @@ bitPackedFile::bitPackedFile(char const *name, uint64 offset, bool forceTruncate fprintf(stderr, "bitPackedFile::bitPackedFile()-- found "); for (uint32 i=0; i<16; i++) fprintf(stderr, "%c", isascii(c[i]) ? c[i] : '.'); - fprintf(stderr, " at position "F_X64"\n", file_offset); + fprintf(stderr, " at position " F_X64 "\n", file_offset); exit(1); } @@ -412,7 +412,7 @@ bitPackedFile::seekNormal(uint64 bitpos) { errno = 0; lseek(_file, _pos * 8 + endianess_offset, SEEK_SET); if (errno) { - fprintf(stderr, "bitPackedFile::seekNormal() '%s' seek to pos="F_U64" failed: %s\n", + fprintf(stderr, "bitPackedFile::seekNormal() '%s' seek to pos=" F_U64 " failed: %s\n", _name, _pos * 8 + endianess_offset, strerror(errno)); exit(1); @@ -421,7 +421,7 @@ bitPackedFile::seekNormal(uint64 bitpos) { errno = 0; size_t wordsread = read(_file, _bfr, sizeof(uint64) * _bfrmax); if (errno) { - fprintf(stderr, "bitPackedFile::seekNormal() '%s' read of "F_U64" bytes failed': %s\n", + fprintf(stderr, "bitPackedFile::seekNormal() '%s' read of " F_U64 " bytes failed': %s\n", _name, sizeof(uint64) * _bfrmax, strerror(errno)); @@ -459,7 +459,7 @@ bitPackedFile::seek(uint64 bitpos) { if ((_pos <= np) && (np <= _pos + _bfrmax - 32)) { _bit = bitpos - (_pos << 6); stat_seekInside++; - //fprintf(stderr, "SEEK INSIDE to _bit="F_U64"\n", _bit); + //fprintf(stderr, "SEEK INSIDE to _bit=" F_U64 "\n", _bit); return; } } @@ -481,7 +481,7 @@ bitPackedFile::seek(uint64 bitpos) { _forceFirstLoad = false; - //fprintf(stderr, "SEEK OUTSIDE to _pos="F_U64" _bit="F_U64"\n", _pos, _bit); + //fprintf(stderr, "SEEK OUTSIDE to _pos=" F_U64 " _bit=" F_U64 "\n", _pos, _bit); } diff --git a/src/AS_UTL/bitPackedFile.H b/src/AS_UTL/bitPackedFile.H index ba415b7d9..14f69cf42 100644 --- a/src/AS_UTL/bitPackedFile.H +++ b/src/AS_UTL/bitPackedFile.H @@ -71,7 +71,7 @@ public: uint64 loadInCore(void); void showStats(FILE *f) { - fprintf(f, "inside: "F_U64" outside: "F_U64"\n", stat_seekInside, stat_seekOutside); + fprintf(f, "inside: " F_U64 " outside: " F_U64 "\n", stat_seekInside, stat_seekOutside); fflush(f); }; private: diff --git a/src/AS_UTL/kMer.C b/src/AS_UTL/kMer.C index d0c8cdf9e..e8da1f01d 100644 --- a/src/AS_UTL/kMer.C +++ b/src/AS_UTL/kMer.C @@ -300,7 +300,7 @@ kMerBuilder::addBaseCompressed(uint64 cf, uint64 cr) { lb = 9; // No valid last base (should probably be ~uint64ZERO, but that screws up diagnostic output) #ifdef DEBUGCOMP - fprintf(stderr, "kMerBuilder::addBaseCompressed()-- lb="uint64FMT" cf="uint64FMT" ms="F_U32" ccl="F_U32" lvl="F_U32"\n", + fprintf(stderr, "kMerBuilder::addBaseCompressed()-- lb="uint64FMT" cf="uint64FMT" ms=" F_U32 " ccl=" F_U32 " lvl=" F_U32 "\n", lb, cf, ms, _compressionCurrentLength, _compression); #endif @@ -392,7 +392,7 @@ kMerBuilder::addBaseCompressed(uint64 cf, uint64 cr) { ms -= _compressionLength[_compressionIndex]; // subtract the count for the letter we just shifted out #ifdef DEBUGCOMP - fprintf(stderr, "kMerBuilder::addBaseCompressed()-- ADDNEWBASE shifted out at idx="F_U32" with "F_U32" positions; final span "F_U32"\n", + fprintf(stderr, "kMerBuilder::addBaseCompressed()-- ADDNEWBASE shifted out at idx=" F_U32 " with " F_U32 " positions; final span " F_U32 "\n", _compressionIndex, _compressionLength[_compressionIndex], ms + 1); diff --git a/src/AS_UTL/kMerHuge.H b/src/AS_UTL/kMerHuge.H index 0347ccce6..357cb3d5d 100644 --- a/src/AS_UTL/kMerHuge.H +++ b/src/AS_UTL/kMerHuge.H @@ -260,7 +260,7 @@ public: val &= uint64MASK(numbits); if (wrd >= KMER_WORDS) { - fprintf(stderr, "kMer::setBits()-- ERROR: tried to set pos="F_U32" numbits="F_U32" larger than KMER_WORDS=%d\n", + fprintf(stderr, "kMer::setBits()-- ERROR: tried to set pos=" F_U32 " numbits=" F_U32 " larger than KMER_WORDS=%d\n", pos, numbits, KMER_WORDS), exit(1); } @@ -274,7 +274,7 @@ public: MERWORD(wrd) |= val << bit; } else { if (wrd+1 >= KMER_WORDS) { - fprintf(stderr, "kMer::setBits()-- ERROR: tried to set pos="F_U32" numbits="F_U32" larger than KMER_WORDS=%d\n", + fprintf(stderr, "kMer::setBits()-- ERROR: tried to set pos=" F_U32 " numbits=" F_U32 " larger than KMER_WORDS=%d\n", pos, numbits, KMER_WORDS), exit(1); } @@ -295,7 +295,7 @@ public: uint32 bit = pos & 0x3f; if (wrd >= KMER_WORDS) { - fprintf(stderr, "kMer::getBits()-- ERROR: tried to get pos="F_U32" numbits="F_U32" larger than KMER_WORDS=%d\n", + fprintf(stderr, "kMer::getBits()-- ERROR: tried to get pos=" F_U32 " numbits=" F_U32 " larger than KMER_WORDS=%d\n", pos, numbits, KMER_WORDS), exit(1); } @@ -303,7 +303,7 @@ public: val = MERWORD(wrd) >> bit; } else { if (wrd+1 >= KMER_WORDS) { - fprintf(stderr, "kMer::getBits()-- ERROR: tried to get pos="F_U32" numbits="F_U32" larger than KMER_WORDS=%d\n", + fprintf(stderr, "kMer::getBits()-- ERROR: tried to get pos=" F_U32 " numbits=" F_U32 " larger than KMER_WORDS=%d\n", pos, numbits, KMER_WORDS), exit(1); } @@ -395,7 +395,7 @@ kMerHuge::setMerSize(uint32 ms) { } if (_maskWord >= KMER_WORDS) { - fprintf(stderr, "kMer::setMerSize()-- ERROR! Desired merSize of "F_U32" larger than\n", _merSize); + fprintf(stderr, "kMer::setMerSize()-- ERROR! Desired merSize of " F_U32 " larger than\n", _merSize); fprintf(stderr, " available storage space (KMER_WORDS=%d, max merSize %d).\n", KMER_WORDS, KMER_WORDS*32); exit(1); } diff --git a/src/AS_UTL/memoryMappedFile.H b/src/AS_UTL/memoryMappedFile.H index 6edd748e0..e88b09b77 100644 --- a/src/AS_UTL/memoryMappedFile.H +++ b/src/AS_UTL/memoryMappedFile.H @@ -109,7 +109,7 @@ public: : mmap(0L, _length, PROT_READ | PROT_WRITE, MAP_FILE | MAP_SHARED, fd, 0); if (errno) - fprintf(stderr, "memoryMappedFile()-- Couldn't mmap '%s' of length "F_SIZE_T": %s\n", _name, _length, strerror(errno)), exit(1); + fprintf(stderr, "memoryMappedFile()-- Couldn't mmap '%s' of length " F_SIZE_T ": %s\n", _name, _length, strerror(errno)), exit(1); close(fd); @@ -135,7 +135,7 @@ public: length = _length - offset; if (offset + length > _length) - fprintf(stderr, "memoryMappedFile()-- Requested "F_SIZE_T" bytes at position "F_SIZE_T" in file '%s', but only "F_SIZE_T" bytes in file.\n", + fprintf(stderr, "memoryMappedFile()-- Requested " F_SIZE_T " bytes at position " F_SIZE_T " in file '%s', but only " F_SIZE_T " bytes in file.\n", length, offset, _name, _length), exit(1); _offset = offset + length; diff --git a/src/AS_UTL/readBuffer.C b/src/AS_UTL/readBuffer.C index 07439217f..9532847b8 100644 --- a/src/AS_UTL/readBuffer.C +++ b/src/AS_UTL/readBuffer.C @@ -176,7 +176,7 @@ readBuffer::fillBuffer(void) { if (errno == EAGAIN) goto again; if (errno) - fprintf(stderr, "readBuffer::fillBuffer()-- only read "F_U64" bytes, couldn't read "F_U64" bytes from '%s': %s\n", + fprintf(stderr, "readBuffer::fillBuffer()-- only read " F_U64 " bytes, couldn't read " F_U64 " bytes from '%s': %s\n", _bufferLen, _bufferMax, _filename, strerror(errno)), exit(1); if (_bufferLen == 0) @@ -209,7 +209,7 @@ readBuffer::seek(uint64 pos) { errno = 0; lseek(_file, pos, SEEK_SET); if (errno) - fprintf(stderr, "readBuffer()-- '%s' couldn't seek to position "F_U64": %s\n", + fprintf(stderr, "readBuffer()-- '%s' couldn't seek to position " F_U64 ": %s\n", _filename, pos, strerror(errno)), exit(1); _bufferLen = 0; @@ -272,7 +272,7 @@ readBuffer::read(void *buf, uint64 len) { errno = 0; bAct = (uint64)::read(_file, bufchar + bCopied + bRead, len - bCopied - bRead); if (errno) - fprintf(stderr, "readBuffer()-- couldn't read "F_U64" bytes from '%s': n%s\n", + fprintf(stderr, "readBuffer()-- couldn't read " F_U64 " bytes from '%s': n%s\n", len, _filename, strerror(errno)), exit(1); // If we hit EOF, return a short read diff --git a/src/AS_UTL/stddev.H b/src/AS_UTL/stddev.H index 94bbb79c3..d27aca52d 100644 --- a/src/AS_UTL/stddev.H +++ b/src/AS_UTL/stddev.H @@ -520,7 +520,7 @@ public: fprintf(F, "#%s\tquantity\n", label); for (uint64 ii=0; ii <= _histogramMax; ii++) - fprintf(F, F_U64"\t"F_U64"\n", ii, _histogram[ii]); + fprintf(F, F_U64"\t" F_U64 "\n", ii, _histogram[ii]); }; diff --git a/src/AS_UTL/sweatShop.C b/src/AS_UTL/sweatShop.C index 81068f29f..e72f2a7d9 100644 --- a/src/AS_UTL/sweatShop.C +++ b/src/AS_UTL/sweatShop.C @@ -150,7 +150,7 @@ sweatShop::setThreadData(uint32 t, void *x) { _workerData = new sweatShopWorker [_numberOfWorkers]; if (t >= _numberOfWorkers) - fprintf(stderr, "sweatShop::setThreadData()-- worker ID "F_U32" more than number of workers="F_U32"\n", t, _numberOfWorkers), exit(1); + fprintf(stderr, "sweatShop::setThreadData()-- worker ID " F_U32 " more than number of workers=" F_U32 "\n", t, _numberOfWorkers), exit(1); _workerData[t].threadUserData = x; } @@ -346,7 +346,7 @@ sweatShop::writer(void) { naptime.tv_sec = 0; naptime.tv_nsec = 5000000ULL; - //fprintf(stderr, "Writer waits for slow thread at "F_U64".\n", _numberOutput); + //fprintf(stderr, "Writer waits for slow thread at " F_U64 ".\n", _numberOutput); nanosleep(&naptime, 0L); } else if (_writerP->_next == 0L) { // Wait for the input. @@ -354,7 +354,7 @@ sweatShop::writer(void) { naptime.tv_sec = 0; naptime.tv_nsec = 5000000ULL; - //fprintf(stderr, "Writer waits for all threads at "F_U64".\n", _numberOutput); + //fprintf(stderr, "Writer waits for all threads at " F_U64 ".\n", _numberOutput); nanosleep(&naptime, 0L); } else { (*_userWriter)(_globalUserData, _writerP->_user); @@ -413,7 +413,7 @@ sweatShop::status(void) { cpuPerSec = _numberComputed / (thisTime - startTime); if (_showStatus) { - fprintf(stderr, " %6.1f/s - %8"F_U64P" loaded; %8"F_U64P" queued for compute; %08"F_U64P" finished; %8"F_U64P" written; %8"F_U64P" queued for output)\r", + fprintf(stderr, " %6.1f/s - %8" F_U64P " loaded; %8" F_U64P " queued for compute; %08" F_U64P " finished; %8" F_U64P " written; %8" F_U64P " queued for output)\r", cpuPerSec, _numberLoaded, deltaCPU, _numberComputed, _numberOutput, deltaOut); fflush(stderr); } @@ -448,7 +448,7 @@ sweatShop::status(void) { cpuPerSec = _numberComputed / (thisTime - startTime); - fprintf(stderr, " %6.1f/s - %08"F_U64P" queued for compute; %08"F_U64P" finished; %08"F_U64P" queued for output)\n", + fprintf(stderr, " %6.1f/s - %08" F_U64P " queued for compute; %08" F_U64P " finished; %08" F_U64P " queued for output)\n", cpuPerSec, deltaCPU, _numberComputed, deltaOut); } @@ -583,7 +583,7 @@ sweatShop::run(void *user, bool beVerbose) { for (uint32 i=0; i<_numberOfWorkers; i++) { err = pthread_create(&_workerData[i].threadID, &threadAttr, _sweatshop_workerThread, _workerData + i); if (err) - fprintf(stderr, "sweatShop::run()-- Failed to launch worker thread "F_U32": %s.\n", i, strerror(err)), exit(1); + fprintf(stderr, "sweatShop::run()-- Failed to launch worker thread " F_U32 ": %s.\n", i, strerror(err)), exit(1); } // Now sit back and relax. @@ -603,7 +603,7 @@ sweatShop::run(void *user, bool beVerbose) { for (uint32 i=0; i<_numberOfWorkers; i++) { err = pthread_join(_workerData[i].threadID, 0L); if (err) - fprintf(stderr, "sweatShop::run()-- Failed to join worker thread "F_U32": %s.\n", i, strerror(err)), exit(1); + fprintf(stderr, "sweatShop::run()-- Failed to join worker thread " F_U32 ": %s.\n", i, strerror(err)), exit(1); } // Cleanup. diff --git a/src/AS_global.C b/src/AS_global.C index 3e5f0c399..a440ddd5e 100644 --- a/src/AS_global.C +++ b/src/AS_global.C @@ -149,7 +149,7 @@ AS_configure(int argc, char **argv) { // Construct a name for this log, and open it. If we can't open it, just skip the log. - sprintf(N, "%s/"F_U64"_%s_"F_U64"_%s", + sprintf(N, "%s/" F_U64 "_%s_" F_U64 "_%s", D, (uint64)time(NULL), H, diff --git a/src/AS_global.H b/src/AS_global.H index 0db9b6d32..62ad5f70f 100644 --- a/src/AS_global.H +++ b/src/AS_global.H @@ -165,27 +165,27 @@ typedef uint64_t uint64; #define F_STRI "%*s" // Integers -#define F_S16 "%"PRId16 -#define F_S16P PRId16 -#define F_S16I "%*"PRId16 -#define F_U16 "%"PRIu16 -#define F_U16P PRIu16 -#define F_U16I "%*"PRIu16 -#define F_S32 "%"PRId32 -#define F_S32P PRId32 -#define F_S32I "%*"PRId32 -#define F_U32 "%"PRIu32 -#define F_U32P PRIu32 -#define F_U32I "%*"PRIu32 -#define F_S64 "%"PRId64 -#define F_S64P PRId64 -#define F_S64I "%*"PRId64 -#define F_U64 "%"PRIu64 -#define F_U64P PRIu64 -#define F_U64I "%*"PRIu64 -#define F_X64 "%016"PRIx64 -#define F_X64P PRIx64 -#define F_X64I "%*"PRIx64 +#define F_S16 "%" PRId16 +#define F_S16P PRId16 +#define F_S16I "%*" PRId16 +#define F_U16 "%" PRIu16 +#define F_U16P PRIu16 +#define F_U16I "%*" PRIu16 +#define F_S32 "%" PRId32 +#define F_S32P PRId32 +#define F_S32I "%*" PRId32 +#define F_U32 "%" PRIu32 +#define F_U32P PRIu32 +#define F_U32I "%*" PRIu32 +#define F_S64 "%" PRId64 +#define F_S64P PRId64 +#define F_S64I "%*" PRId64 +#define F_U64 "%" PRIu64 +#define F_U64P PRIu64 +#define F_U64I "%*" PRIu64 +#define F_X64 "%016" PRIx64 +#define F_X64P PRIx64 +#define F_X64I "%*" PRIx64 // Floating points #define F_F32 "%f" @@ -204,15 +204,6 @@ typedef uint64_t uint64; #define F_OFF_TP F_S64P #define F_OFF_TI F_S64I -typedef uintptr_t INTPTR; - - -// These are used to pad various structs to specific sizes -#if ULONG_MAX == 0xffffffff -#define TRUE32BIT -#else -#define TRUE64BIT -#endif #if defined(_FILE_OFFSET_BITS) && (_FILE_OFFSET_BITS == 32) @@ -220,10 +211,6 @@ typedef uintptr_t INTPTR; #endif -// Enable troublesome asserts. These typically have work arounds, and occasionally trigger. -// They're really only useful if the assembly can be debugged. -#undef AGGRESSIVE_ASSERT - // perl's chomp is pretty nice // Not a great place to put this, but it's getting used all over. diff --git a/src/bogart/AS_BAT_AssemblyGraph.C b/src/bogart/AS_BAT_AssemblyGraph.C index b1c1b5e29..51d79fb04 100644 --- a/src/bogart/AS_BAT_AssemblyGraph.C +++ b/src/bogart/AS_BAT_AssemblyGraph.C @@ -751,13 +751,13 @@ AssemblyGraph::filterEdges(TigVector &tigs) { // Report - writeStatus("AssemblyGraph()-- "F_U64" contig edges and "F_U64" unitig edges.\n", nContig, nUnitig); - writeStatus("AssemblyGraph()-- "F_U64" bubble edges and "F_U64" repeat edges.\n", nBubble, nRepeat); - writeStatus("AssemblyGraph()-- "F_U64" middle contig edges filtered from "F_U64" reads.\n", nMiddleFiltered, nMiddleReads); - writeStatus("AssemblyGraph()-- "F_U64" repeat end edges filtered from "F_U64" reads.\n", nRepeatFiltered, nRepeatReads); - writeStatus("AssemblyGraph()-- "F_U64" repeat edges (not output).\n", nRepeatEdges); - writeStatus("AssemblyGraph()-- "F_U64" bubble edges.\n", nBubbleEdges); - writeStatus("AssemblyGraph()-- "F_U64" intersecting edges (from the end of a tig to somewhere else).\n", nIntersecting); + writeStatus("AssemblyGraph()-- " F_U64 " contig edges and " F_U64 " unitig edges.\n", nContig, nUnitig); + writeStatus("AssemblyGraph()-- " F_U64 " bubble edges and " F_U64 " repeat edges.\n", nBubble, nRepeat); + writeStatus("AssemblyGraph()-- " F_U64 " middle contig edges filtered from " F_U64 " reads.\n", nMiddleFiltered, nMiddleReads); + writeStatus("AssemblyGraph()-- " F_U64 " repeat end edges filtered from " F_U64 " reads.\n", nRepeatFiltered, nRepeatReads); + writeStatus("AssemblyGraph()-- " F_U64 " repeat edges (not output).\n", nRepeatEdges); + writeStatus("AssemblyGraph()-- " F_U64 " bubble edges.\n", nBubbleEdges); + writeStatus("AssemblyGraph()-- " F_U64 " intersecting edges (from the end of a tig to somewhere else).\n", nIntersecting); } @@ -854,7 +854,7 @@ AssemblyGraph::reportReadGraph(TigVector &tigs, const char *prefix, const char * } } - writeStatus("AssemblyGraph()-- Found "F_U64" edges to unassembled contigs.\n", nEdgeToUnasm); + writeStatus("AssemblyGraph()-- Found " F_U64 " edges to unassembled contigs.\n", nEdgeToUnasm); // Then write those sequences. @@ -953,12 +953,12 @@ AssemblyGraph::reportReadGraph(TigVector &tigs, const char *prefix, const char * // And report statistics. - writeStatus("AssemblyGraph()-- %8"F_U64P" bubble placements\n", nBubble); - writeStatus("AssemblyGraph()-- %8"F_U64P" repeat placements\n", nRepeat); + writeStatus("AssemblyGraph()-- %8" F_U64P " bubble placements\n", nBubble); + writeStatus("AssemblyGraph()-- %8" F_U64P " repeat placements\n", nRepeat); writeStatus("\n"); - writeStatus("AssemblyGraph()-- Intratig edges: %8"F_U64P" contained %8"F_U64P" 5' %8"F_U64P" 3' (in both contig and unitig)\n", nTig[0], nTig[1], nTig[2]); - writeStatus("AssemblyGraph()-- Contig only edges: %8"F_U64P" contained %8"F_U64P" 5' %8"F_U64P" 3'\n", nCtg[0], nCtg[1], nCtg[2]); - writeStatus("AssemblyGraph()-- Unitig only edges: %8"F_U64P" contained %8"F_U64P" 5' %8"F_U64P" 3'\n", nUtg[0], nUtg[1], nUtg[2]); - writeStatus("AssemblyGraph()-- Intercontig edges: %8"F_U64P" contained %8"F_U64P" 5' %8"F_U64P" 3' (in neither contig nor unitig)\n", nAsm[0], nAsm[1], nAsm[2]); + writeStatus("AssemblyGraph()-- Intratig edges: %8" F_U64P " contained %8" F_U64P " 5' %8" F_U64P " 3' (in both contig and unitig)\n", nTig[0], nTig[1], nTig[2]); + writeStatus("AssemblyGraph()-- Contig only edges: %8" F_U64P " contained %8" F_U64P " 5' %8" F_U64P " 3'\n", nCtg[0], nCtg[1], nCtg[2]); + writeStatus("AssemblyGraph()-- Unitig only edges: %8" F_U64P " contained %8" F_U64P " 5' %8" F_U64P " 3'\n", nUtg[0], nUtg[1], nUtg[2]); + writeStatus("AssemblyGraph()-- Intercontig edges: %8" F_U64P " contained %8" F_U64P " 5' %8" F_U64P " 3' (in neither contig nor unitig)\n", nAsm[0], nAsm[1], nAsm[2]); } diff --git a/src/bogart/AS_BAT_BestOverlapGraph.C b/src/bogart/AS_BAT_BestOverlapGraph.C index da5f33977..5743a9f9a 100644 --- a/src/bogart/AS_BAT_BestOverlapGraph.C +++ b/src/bogart/AS_BAT_BestOverlapGraph.C @@ -108,7 +108,7 @@ BestOverlapGraph::removeSuspicious(const char *UNUSED(prefix)) { } } - writeStatus("BestOverlapGraph()-- marked "F_U64" reads as suspicious.\n", _suspicious.size()); + writeStatus("BestOverlapGraph()-- marked " F_U64 " reads as suspicious.\n", _suspicious.size()); } @@ -330,7 +330,7 @@ BestOverlapGraph::removeSpurs(const char *prefix) { _spur.insert(fi); } - writeStatus("BestOverlapGraph()-- detected "F_SIZE_T" spur reads.\n", _spur.size()); + writeStatus("BestOverlapGraph()-- detected " F_SIZE_T " spur reads.\n", _spur.size()); if (F) fclose(F); @@ -398,7 +398,7 @@ BestOverlapGraph::BestOverlapGraph(double erateGraph, const char *prefix) { writeStatus("\n"); - writeStatus("BestOverlapGraph()-- allocating best edges ("F_SIZE_T"MB)\n", + writeStatus("BestOverlapGraph()-- allocating best edges (" F_SIZE_T "MB)\n", ((2 * sizeof(BestEdgeOverlap) * (RI->numReads() + 1)) >> 20)); _bestA = new BestOverlaps [RI->numReads() + 1]; // Cleared in findEdges() @@ -806,7 +806,7 @@ BestOverlapGraph::scoreEdge(BAToverlap& olap) { if (isOverlapBadQuality(olap)) { // Yuck. Don't want to use this crud. if ((enableLog == true) && (logFileFlagSet(LOG_OVERLAP_SCORING))) - writeLog("scoreEdge()-- OVERLAP BADQ: %d %d %c hangs "F_S32" "F_S32" err %.3f -- bad quality\n", + writeLog("scoreEdge()-- OVERLAP BADQ: %d %d %c hangs " F_S32 " " F_S32 " err %.3f -- bad quality\n", olap.a_iid, olap.b_iid, olap.flipped ? 'A' : 'N', olap.a_hang, olap.b_hang, olap.erate()); return; } @@ -814,7 +814,7 @@ BestOverlapGraph::scoreEdge(BAToverlap& olap) { if (isOverlapRestricted(olap)) { // Whoops, don't want this overlap for this BOG if ((enableLog == true) && (logFileFlagSet(LOG_OVERLAP_SCORING))) - writeLog("scoreEdge()-- OVERLAP RESTRICT: %d %d %c hangs "F_S32" "F_S32" err %.3f -- restricted\n", + writeLog("scoreEdge()-- OVERLAP RESTRICT: %d %d %c hangs " F_S32 " " F_S32 " err %.3f -- restricted\n", olap.a_iid, olap.b_iid, olap.flipped ? 'A' : 'N', olap.a_hang, olap.b_hang, olap.erate()); return; } @@ -822,7 +822,7 @@ BestOverlapGraph::scoreEdge(BAToverlap& olap) { if (isSuspicious(olap.b_iid)) { // Whoops, don't want this overlap for this BOG if ((enableLog == true) && (logFileFlagSet(LOG_OVERLAP_SCORING))) - writeLog("scoreEdge()-- OVERLAP SUSP: %d %d %c hangs "F_S32" "F_S32" err %.3f -- suspicious\n", + writeLog("scoreEdge()-- OVERLAP SUSP: %d %d %c hangs " F_S32 " " F_S32 " err %.3f -- suspicious\n", olap.a_iid, olap.b_iid, olap.flipped ? 'A' : 'N', olap.a_hang, olap.b_hang, olap.erate()); return; } @@ -831,7 +831,7 @@ BestOverlapGraph::scoreEdge(BAToverlap& olap) { ((olap.a_hang <= 0) && (olap.b_hang >= 0))) { // Skip containment overlaps. if ((enableLog == true) && (logFileFlagSet(LOG_OVERLAP_SCORING))) - writeLog("scoreEdge()-- OVERLAP CONT: %d %d %c hangs "F_S32" "F_S32" err %.3f -- container read\n", + writeLog("scoreEdge()-- OVERLAP CONT: %d %d %c hangs " F_S32 " " F_S32 " err %.3f -- container read\n", olap.a_iid, olap.b_iid, olap.flipped ? 'A' : 'N', olap.a_hang, olap.b_hang, olap.erate()); return; } @@ -839,7 +839,7 @@ BestOverlapGraph::scoreEdge(BAToverlap& olap) { if (isContained(olap.b_iid) == true) { // Skip overlaps to contained reads (allow scoring of best edges from contained reads). if ((enableLog == true) && (logFileFlagSet(LOG_OVERLAP_SCORING))) - writeLog("scoreEdge()-- OVERLAP CONT: %d %d %c hangs "F_S32" "F_S32" err %.3f -- contained read\n", + writeLog("scoreEdge()-- OVERLAP CONT: %d %d %c hangs " F_S32 " " F_S32 " err %.3f -- contained read\n", olap.a_iid, olap.b_iid, olap.flipped ? 'A' : 'N', olap.a_hang, olap.b_hang, olap.erate()); return; } @@ -853,7 +853,7 @@ BestOverlapGraph::scoreEdge(BAToverlap& olap) { if (newScr <= score) { if ((enableLog == true) && (logFileFlagSet(LOG_OVERLAP_SCORING))) - writeLog("scoreEdge()-- OVERLAP GOOD: %d %d %c hangs "F_S32" "F_S32" err %.3f -- no better than best\n", + writeLog("scoreEdge()-- OVERLAP GOOD: %d %d %c hangs " F_S32 " " F_S32 " err %.3f -- no better than best\n", olap.a_iid, olap.b_iid, olap.flipped ? 'A' : 'N', olap.a_hang, olap.b_hang, olap.erate()); return; } @@ -863,7 +863,7 @@ BestOverlapGraph::scoreEdge(BAToverlap& olap) { score = newScr; if ((enableLog == true) && (logFileFlagSet(LOG_OVERLAP_SCORING))) - writeLog("scoreEdge()-- OVERLAP BEST: %d %d %c hangs "F_S32" "F_S32" err %.3f -- NOW BEST\n", + writeLog("scoreEdge()-- OVERLAP BEST: %d %d %c hangs " F_S32 " " F_S32 " err %.3f -- NOW BEST\n", olap.a_iid, olap.b_iid, olap.flipped ? 'A' : 'N', olap.a_hang, olap.b_hang, olap.erate()); } @@ -891,7 +891,7 @@ BestOverlapGraph::isOverlapBadQuality(BAToverlap& olap) { if (olap.erate() <= _errorLimit) { if ((enableLog == true) && (logFileFlagSet(LOG_OVERLAP_SCORING))) - writeLog("isOverlapBadQuality()-- OVERLAP GOOD: %d %d %c hangs "F_S32" "F_S32" err %.3f\n", + writeLog("isOverlapBadQuality()-- OVERLAP GOOD: %d %d %c hangs " F_S32 " " F_S32 " err %.3f\n", olap.a_iid, olap.b_iid, olap.flipped ? 'A' : 'N', olap.a_hang, @@ -906,7 +906,7 @@ BestOverlapGraph::isOverlapBadQuality(BAToverlap& olap) { // error rate above a few percent. canu doesn't do short overlaps. if ((enableLog == true) && (logFileFlagSet(LOG_OVERLAP_SCORING))) - writeLog("isOverlapBadQuality()-- OVERLAP REJECTED: %d %d %c hangs "F_S32" "F_S32" err %.3f\n", + writeLog("isOverlapBadQuality()-- OVERLAP REJECTED: %d %d %c hangs " F_S32 " " F_S32 " err %.3f\n", olap.a_iid, olap.b_iid, olap.flipped ? 'A' : 'N', olap.a_hang, diff --git a/src/bogart/AS_BAT_Instrumentation.C b/src/bogart/AS_BAT_Instrumentation.C index 21f2fcc0a..a53fa44fe 100644 --- a/src/bogart/AS_BAT_Instrumentation.C +++ b/src/bogart/AS_BAT_Instrumentation.C @@ -146,7 +146,7 @@ classifyTigsAsUnassembled(TigVector &tigs, // Rule 1. Too few reads. if (utg->ufpath.size() < fewReadsNumber) { - fprintf(F, "unitig "F_U32" unassembled - too few reads ("F_U64" < "F_U32")\n", ti, utg->ufpath.size(), fewReadsNumber); + fprintf(F, "unitig " F_U32 " unassembled - too few reads (" F_U64 " < " F_U32 ")\n", ti, utg->ufpath.size(), fewReadsNumber); utg->_isUnassembled = true; nTooFew += 1; bTooFew += utg->getLength(); @@ -156,7 +156,7 @@ classifyTigsAsUnassembled(TigVector &tigs, // Rule 2. Short. if (utg->getLength() < tooShortLength) { - fprintf(F, "unitig "F_U32" unassembled - too short ("F_U32" < "F_U32")\n", ti, utg->getLength(), tooShortLength); + fprintf(F, "unitig " F_U32 " unassembled - too short (" F_U32 " < " F_U32 ")\n", ti, utg->getLength(), tooShortLength); utg->_isUnassembled = true; nShort += 1; bShort += utg->getLength(); @@ -172,7 +172,7 @@ classifyTigsAsUnassembled(TigVector &tigs, int frgend = MAX(frg->position.bgn, frg->position.end); if (frgend - frgbgn > utg->getLength() * spanFraction) { - fprintf(F, "unitig "F_U32" unassembled - single read spans unitig (read "F_U32" "F_U32"-"F_U32" spans fraction %f > %f\n", + fprintf(F, "unitig " F_U32 " unassembled - single read spans unitig (read " F_U32 " " F_U32 "-" F_U32 " spans fraction %f > %f\n", ti, frg->ident, frg->position.bgn, frg->position.end, (double)(frgend - frgbgn) / utg->getLength(), spanFraction); utg->_isUnassembled = true; nSingle += 1; @@ -210,7 +210,7 @@ classifyTigsAsUnassembled(TigVector &tigs, double lowcov = (double)basesLow / (basesLow + basesHigh); if (lowcov >= lowcovFraction) { - fprintf(F, "Unitig "F_U32" unassembled - low coverage (%.4f > %.4f at < "F_U32"x coverage)\n", + fprintf(F, "Unitig " F_U32 " unassembled - low coverage (%.4f > %.4f at < " F_U32 "x coverage)\n", ti, lowcov, lowcovFraction, lowcovDepth); utg->_isUnassembled = true; nCoverage += 1; @@ -250,7 +250,7 @@ reportN50(FILE *F, vector &data, char const *label, uint64 genomeSize) { for (uint64 i=0; i 0) @@ -262,7 +262,7 @@ reportN50(FILE *F, vector &data, char const *label, uint64 genomeSize) { sum += data[i]; while (siz * nnn / 100 < sum) { - fprintf(F, "ng%03"F_U64P" %9"F_U32P" lg%03"F_U64P" %8"F_U64P" sum %11"F_U64P" (%s)\n", + fprintf(F, "ng%03" F_U64P " %9" F_U32P " lg%03" F_U64P " %8" F_U64P " sum %11" F_U64P " (%s)\n", nnn, data[i], nnn, i+1, sum, @@ -620,64 +620,64 @@ reportOverlaps(TigVector &tigs, const char *prefix, const char *name) { fprintf(F, "=====================================\n"); fprintf(F, "OVERLAP COUNTS\n"); fprintf(F, "\n"); - fprintf(F, "dovetail overlaps (best) "F_U64"\n", bb->total); - fprintf(F, "dovetail overlaps "F_U64"\n", dd->total); - fprintf(F, "dovetail overlaps to contained reads "F_U64"\n", dc->total); - fprintf(F, "containment overlaps "F_U64"\n", cc->total); + fprintf(F, "dovetail overlaps (best) " F_U64 "\n", bb->total); + fprintf(F, "dovetail overlaps " F_U64 "\n", dd->total); + fprintf(F, "dovetail overlaps to contained reads " F_U64 "\n", dc->total); + fprintf(F, "containment overlaps " F_U64 "\n", cc->total); fprintf(F, "\n"); fprintf(F, "=====================================\n"); fprintf(F, "BEST EDGE OVERLAP FATE\n"); fprintf(F, "\n"); fprintf(F, "SATISFIED best edges DOVETAIL\n"); fprintf(F, "--------- ------------ -------\n"); - fprintf(F, "same-contig %12"F_U64P" %6.2f%%\n", bb->doveSatSame[tCTG], B(bb->doveSatSame[tCTG])); - fprintf(F, "same-repeat %12"F_U64P" %6.2f%%\n", bb->doveSatSame[tRPT], B(bb->doveSatSame[tRPT])); - fprintf(F, "same-bubble %12"F_U64P" %6.2f%%\n", bb->doveSatSame[tBUB], B(bb->doveSatSame[tBUB])); + fprintf(F, "same-contig %12" F_U64P " %6.2f%%\n", bb->doveSatSame[tCTG], B(bb->doveSatSame[tCTG])); + fprintf(F, "same-repeat %12" F_U64P " %6.2f%%\n", bb->doveSatSame[tRPT], B(bb->doveSatSame[tRPT])); + fprintf(F, "same-bubble %12" F_U64P " %6.2f%%\n", bb->doveSatSame[tBUB], B(bb->doveSatSame[tBUB])); fprintf(F, "\n"); fprintf(F, "UNSATISFIED best edges DOVETAIL\n"); fprintf(F, "----------- ------------ -------\n"); - fprintf(F, "same-contig %12"F_U64P" %6.2f%%\n", bb->doveUnsatSame[tCTG], B(bb->doveUnsatSame[tCTG])); - fprintf(F, "same-repeat %12"F_U64P" %6.2f%%\n", bb->doveUnsatSame[tRPT], B(bb->doveUnsatSame[tRPT])); - fprintf(F, "same-bubble %12"F_U64P" %6.2f%%\n", bb->doveUnsatSame[tBUB], B(bb->doveUnsatSame[tBUB])); - fprintf(F, "same-unassembled %12"F_U64P" %6.2f%%\n", bb->doveUnsatSame[tUNA], B(bb->doveUnsatSame[tUNA])); - fprintf(F, "same-unused %12"F_U64P" %6.2f%%\n", bb->doveUnsatSame[tUNU], B(bb->doveUnsatSame[tUNU])); + fprintf(F, "same-contig %12" F_U64P " %6.2f%%\n", bb->doveUnsatSame[tCTG], B(bb->doveUnsatSame[tCTG])); + fprintf(F, "same-repeat %12" F_U64P " %6.2f%%\n", bb->doveUnsatSame[tRPT], B(bb->doveUnsatSame[tRPT])); + fprintf(F, "same-bubble %12" F_U64P " %6.2f%%\n", bb->doveUnsatSame[tBUB], B(bb->doveUnsatSame[tBUB])); + fprintf(F, "same-unassembled %12" F_U64P " %6.2f%%\n", bb->doveUnsatSame[tUNA], B(bb->doveUnsatSame[tUNA])); + fprintf(F, "same-unused %12" F_U64P " %6.2f%%\n", bb->doveUnsatSame[tUNU], B(bb->doveUnsatSame[tUNU])); fprintf(F, "\n"); fprintf(F, "UNSATISFIED best edges DOVETAIL\n"); fprintf(F, "----------- ------------ -------\n"); - fprintf(F, "contig-contig %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tCTG][tCTG], B(bb->doveUnsatDiff[tCTG][tCTG])); - fprintf(F, "contig-repeat %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tCTG][tRPT], B(bb->doveUnsatDiff[tCTG][tRPT])); - fprintf(F, "contig-bubble %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tCTG][tBUB], B(bb->doveUnsatDiff[tCTG][tBUB])); - fprintf(F, "contig-unassembled %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tCTG][tUNA], B(bb->doveUnsatDiff[tCTG][tUNA])); - fprintf(F, "contig-unused %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tCTG][tUNU], B(bb->doveUnsatDiff[tCTG][tUNU])); - fprintf(F, "contig-none %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tCTG][tNOP], B(bb->doveUnsatDiff[tCTG][tNOP])); + fprintf(F, "contig-contig %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tCTG][tCTG], B(bb->doveUnsatDiff[tCTG][tCTG])); + fprintf(F, "contig-repeat %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tCTG][tRPT], B(bb->doveUnsatDiff[tCTG][tRPT])); + fprintf(F, "contig-bubble %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tCTG][tBUB], B(bb->doveUnsatDiff[tCTG][tBUB])); + fprintf(F, "contig-unassembled %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tCTG][tUNA], B(bb->doveUnsatDiff[tCTG][tUNA])); + fprintf(F, "contig-unused %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tCTG][tUNU], B(bb->doveUnsatDiff[tCTG][tUNU])); + fprintf(F, "contig-none %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tCTG][tNOP], B(bb->doveUnsatDiff[tCTG][tNOP])); fprintf(F, "\n"); -//fprintf(F, "repeat-contig %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tRPT][tCTG], B(bb->doveUnsatDiff[tRPT][tCTG])); - fprintf(F, "repeat-repeat %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tRPT][tRPT], B(bb->doveUnsatDiff[tRPT][tRPT])); - fprintf(F, "repeat-bubble %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tRPT][tBUB], B(bb->doveUnsatDiff[tRPT][tBUB])); - fprintf(F, "repeat-unassembled %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tRPT][tUNA], B(bb->doveUnsatDiff[tRPT][tUNA])); - fprintf(F, "repeat-unused %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tRPT][tUNU], B(bb->doveUnsatDiff[tRPT][tUNU])); - fprintf(F, "repeat-none %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tRPT][tNOP], B(bb->doveUnsatDiff[tRPT][tNOP])); +//fprintf(F, "repeat-contig %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tRPT][tCTG], B(bb->doveUnsatDiff[tRPT][tCTG])); + fprintf(F, "repeat-repeat %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tRPT][tRPT], B(bb->doveUnsatDiff[tRPT][tRPT])); + fprintf(F, "repeat-bubble %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tRPT][tBUB], B(bb->doveUnsatDiff[tRPT][tBUB])); + fprintf(F, "repeat-unassembled %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tRPT][tUNA], B(bb->doveUnsatDiff[tRPT][tUNA])); + fprintf(F, "repeat-unused %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tRPT][tUNU], B(bb->doveUnsatDiff[tRPT][tUNU])); + fprintf(F, "repeat-none %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tRPT][tNOP], B(bb->doveUnsatDiff[tRPT][tNOP])); fprintf(F, "\n"); -//fprintf(F, "bubble-contig %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tBUB][tCTG], B(bb->doveUnsatDiff[tBUB][tCTG])); -//fprintf(F, "bubble-repeat %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tBUB][tRPT], B(bb->doveUnsatDiff[tBUB][tRPT])); - fprintf(F, "bubble-bubble %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tBUB][tBUB], B(bb->doveUnsatDiff[tBUB][tBUB])); - fprintf(F, "bubble-unassembled %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tBUB][tUNA], B(bb->doveUnsatDiff[tBUB][tUNA])); - fprintf(F, "bubble-unused %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tBUB][tUNU], B(bb->doveUnsatDiff[tBUB][tUNU])); - fprintf(F, "bubble-none %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tBUB][tNOP], B(bb->doveUnsatDiff[tBUB][tNOP])); +//fprintf(F, "bubble-contig %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tBUB][tCTG], B(bb->doveUnsatDiff[tBUB][tCTG])); +//fprintf(F, "bubble-repeat %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tBUB][tRPT], B(bb->doveUnsatDiff[tBUB][tRPT])); + fprintf(F, "bubble-bubble %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tBUB][tBUB], B(bb->doveUnsatDiff[tBUB][tBUB])); + fprintf(F, "bubble-unassembled %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tBUB][tUNA], B(bb->doveUnsatDiff[tBUB][tUNA])); + fprintf(F, "bubble-unused %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tBUB][tUNU], B(bb->doveUnsatDiff[tBUB][tUNU])); + fprintf(F, "bubble-none %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tBUB][tNOP], B(bb->doveUnsatDiff[tBUB][tNOP])); fprintf(F, "\n"); -//fprintf(F, "unassembled-contig %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tUNA][tCTG], B(bb->doveUnsatDiff[tUNA][tCTG])); -//fprintf(F, "unassembled-repeat %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tUNA][tRPT], B(bb->doveUnsatDiff[tUNA][tRPT])); -//fprintf(F, "unassembled-bubble %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tUNA][tBUB], B(bb->doveUnsatDiff[tUNA][tBUB])); - fprintf(F, "unassembled-unassembled %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tUNA][tUNA], B(bb->doveUnsatDiff[tUNA][tUNA])); - fprintf(F, "unassembled-unused %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tUNA][tUNU], B(bb->doveUnsatDiff[tUNA][tUNU])); - fprintf(F, "unassembled-none %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tUNA][tNOP], B(bb->doveUnsatDiff[tUNA][tNOP])); +//fprintf(F, "unassembled-contig %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tUNA][tCTG], B(bb->doveUnsatDiff[tUNA][tCTG])); +//fprintf(F, "unassembled-repeat %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tUNA][tRPT], B(bb->doveUnsatDiff[tUNA][tRPT])); +//fprintf(F, "unassembled-bubble %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tUNA][tBUB], B(bb->doveUnsatDiff[tUNA][tBUB])); + fprintf(F, "unassembled-unassembled %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tUNA][tUNA], B(bb->doveUnsatDiff[tUNA][tUNA])); + fprintf(F, "unassembled-unused %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tUNA][tUNU], B(bb->doveUnsatDiff[tUNA][tUNU])); + fprintf(F, "unassembled-none %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tUNA][tNOP], B(bb->doveUnsatDiff[tUNA][tNOP])); fprintf(F, "\n"); -//fprintf(F, "unused-contig %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tUNU][tCTG], B(bb->doveUnsatDiff[tUNU][tCTG])) -//fprintf(F, "unused-repeat %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tUNU][tRPT], B(bb->doveUnsatDiff[tUNU][tRPT])); -//fprintf(F, "unused-bubble %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tUNU][tBUB], B(bb->doveUnsatDiff[tUNU][tBUB])); -//fprintf(F, "unused-unassembled %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tUNU][tUNA], B(bb->doveUnsatDiff[tUNU][tUNA])); - fprintf(F, "unused-unused %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tUNU][tUNU], B(bb->doveUnsatDiff[tUNU][tUNU])); - fprintf(F, "unused-none %12"F_U64P" %6.2f%%\n", bb->doveUnsatDiff[tUNU][tNOP], B(bb->doveUnsatDiff[tUNU][tNOP])); +//fprintf(F, "unused-contig %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tUNU][tCTG], B(bb->doveUnsatDiff[tUNU][tCTG])) +//fprintf(F, "unused-repeat %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tUNU][tRPT], B(bb->doveUnsatDiff[tUNU][tRPT])); +//fprintf(F, "unused-bubble %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tUNU][tBUB], B(bb->doveUnsatDiff[tUNU][tBUB])); +//fprintf(F, "unused-unassembled %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tUNU][tUNA], B(bb->doveUnsatDiff[tUNU][tUNA])); + fprintf(F, "unused-unused %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tUNU][tUNU], B(bb->doveUnsatDiff[tUNU][tUNU])); + fprintf(F, "unused-none %12" F_U64P " %6.2f%%\n", bb->doveUnsatDiff[tUNU][tNOP], B(bb->doveUnsatDiff[tUNU][tNOP])); fprintf(F, "\n"); fprintf(F, "\n"); fprintf(F, "=====================================\n"); @@ -685,49 +685,49 @@ reportOverlaps(TigVector &tigs, const char *prefix, const char *name) { fprintf(F, "\n"); fprintf(F, "SATISFIED all overlaps DOVETAIL DOVECONT CONTAINMENT\n"); fprintf(F, "--------- ------------ ------- ------------ ------- ------------ -------\n"); - fprintf(F, "same-contig %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveSatSame[tCTG], P(dd->doveSatSame[tCTG]), dc->doveSatSame[tCTG], Q(dc->doveSatSame[tCTG]), cc->contSatSame[tCTG], R(cc->contSatSame[tCTG])); - fprintf(F, "same-repeat %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveSatSame[tRPT], P(dd->doveSatSame[tRPT]), dc->doveSatSame[tRPT], Q(dc->doveSatSame[tRPT]), cc->contSatSame[tRPT], R(cc->contSatSame[tRPT])); - fprintf(F, "same-bubble %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveSatSame[tBUB], P(dd->doveSatSame[tBUB]), dc->doveSatSame[tBUB], Q(dc->doveSatSame[tBUB]), cc->contSatSame[tBUB], R(cc->contSatSame[tBUB])); + fprintf(F, "same-contig %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveSatSame[tCTG], P(dd->doveSatSame[tCTG]), dc->doveSatSame[tCTG], Q(dc->doveSatSame[tCTG]), cc->contSatSame[tCTG], R(cc->contSatSame[tCTG])); + fprintf(F, "same-repeat %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveSatSame[tRPT], P(dd->doveSatSame[tRPT]), dc->doveSatSame[tRPT], Q(dc->doveSatSame[tRPT]), cc->contSatSame[tRPT], R(cc->contSatSame[tRPT])); + fprintf(F, "same-bubble %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveSatSame[tBUB], P(dd->doveSatSame[tBUB]), dc->doveSatSame[tBUB], Q(dc->doveSatSame[tBUB]), cc->contSatSame[tBUB], R(cc->contSatSame[tBUB])); fprintf(F, "\n"); fprintf(F, "UNSATISFIED all overlaps DOVETAIL DOVECONT CONTAINMENT\n"); fprintf(F, "----------- ------------ ------- ------------ ------- ------------ -------\n"); - fprintf(F, "same-contig %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatSame[tCTG], P(dd->doveUnsatSame[tCTG]), dc->doveUnsatSame[tCTG], Q(dc->doveUnsatSame[tCTG]), cc->contUnsatSame[tCTG], R(cc->contUnsatSame[tCTG])); - fprintf(F, "same-repeat %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatSame[tRPT], P(dd->doveUnsatSame[tRPT]), dc->doveUnsatSame[tRPT], Q(dc->doveUnsatSame[tRPT]), cc->contUnsatSame[tRPT], R(cc->contUnsatSame[tRPT])); - fprintf(F, "same-bubble %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatSame[tBUB], P(dd->doveUnsatSame[tBUB]), dc->doveUnsatSame[tBUB], Q(dc->doveUnsatSame[tBUB]), cc->contUnsatSame[tBUB], R(cc->contUnsatSame[tBUB])); - fprintf(F, "same-unassembled %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatSame[tUNA], P(dd->doveUnsatSame[tUNA]), dc->doveUnsatSame[tUNA], Q(dc->doveUnsatSame[tUNA]), cc->contUnsatSame[tUNA], R(cc->contUnsatSame[tUNA])); - fprintf(F, "same-unused %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatSame[tUNU], P(dd->doveUnsatSame[tUNU]), dc->doveUnsatSame[tUNU], Q(dc->doveUnsatSame[tUNU]), cc->contUnsatSame[tUNU], R(cc->contUnsatSame[tUNU])); + fprintf(F, "same-contig %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatSame[tCTG], P(dd->doveUnsatSame[tCTG]), dc->doveUnsatSame[tCTG], Q(dc->doveUnsatSame[tCTG]), cc->contUnsatSame[tCTG], R(cc->contUnsatSame[tCTG])); + fprintf(F, "same-repeat %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatSame[tRPT], P(dd->doveUnsatSame[tRPT]), dc->doveUnsatSame[tRPT], Q(dc->doveUnsatSame[tRPT]), cc->contUnsatSame[tRPT], R(cc->contUnsatSame[tRPT])); + fprintf(F, "same-bubble %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatSame[tBUB], P(dd->doveUnsatSame[tBUB]), dc->doveUnsatSame[tBUB], Q(dc->doveUnsatSame[tBUB]), cc->contUnsatSame[tBUB], R(cc->contUnsatSame[tBUB])); + fprintf(F, "same-unassembled %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatSame[tUNA], P(dd->doveUnsatSame[tUNA]), dc->doveUnsatSame[tUNA], Q(dc->doveUnsatSame[tUNA]), cc->contUnsatSame[tUNA], R(cc->contUnsatSame[tUNA])); + fprintf(F, "same-unused %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatSame[tUNU], P(dd->doveUnsatSame[tUNU]), dc->doveUnsatSame[tUNU], Q(dc->doveUnsatSame[tUNU]), cc->contUnsatSame[tUNU], R(cc->contUnsatSame[tUNU])); fprintf(F, "\n"); fprintf(F, "UNSATISFIED all overlaps DOVETAIL DOVECONT CONTAINMENT\n"); fprintf(F, "----------- ------------ ------- ------------ ------- ------------ -------\n"); - fprintf(F, "contig-contig %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tCTG][tCTG], P(dd->doveUnsatDiff[tCTG][tCTG]), dc->doveUnsatDiff[tCTG][tCTG], Q(dc->doveUnsatDiff[tCTG][tCTG]), cc->contUnsatDiff[tCTG][tCTG], R(cc->contUnsatDiff[tCTG][tCTG])); - fprintf(F, "contig-repeat %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tCTG][tRPT], P(dd->doveUnsatDiff[tCTG][tRPT]), dc->doveUnsatDiff[tCTG][tRPT], Q(dc->doveUnsatDiff[tCTG][tRPT]), cc->contUnsatDiff[tCTG][tRPT], R(cc->contUnsatDiff[tCTG][tRPT])); - fprintf(F, "contig-bubble %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tCTG][tBUB], P(dd->doveUnsatDiff[tCTG][tBUB]), dc->doveUnsatDiff[tCTG][tBUB], Q(dc->doveUnsatDiff[tCTG][tBUB]), cc->contUnsatDiff[tCTG][tBUB], R(cc->contUnsatDiff[tCTG][tBUB])); - fprintf(F, "contig-unassembled %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tCTG][tUNA], P(dd->doveUnsatDiff[tCTG][tUNA]), dc->doveUnsatDiff[tCTG][tUNA], Q(dc->doveUnsatDiff[tCTG][tUNA]), cc->contUnsatDiff[tCTG][tUNA], R(cc->contUnsatDiff[tCTG][tUNA])); - fprintf(F, "contig-unused %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tCTG][tUNU], P(dd->doveUnsatDiff[tCTG][tUNU]), dc->doveUnsatDiff[tCTG][tUNU], Q(dc->doveUnsatDiff[tCTG][tUNU]), cc->contUnsatDiff[tCTG][tUNU], R(cc->contUnsatDiff[tCTG][tUNU])); + fprintf(F, "contig-contig %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tCTG][tCTG], P(dd->doveUnsatDiff[tCTG][tCTG]), dc->doveUnsatDiff[tCTG][tCTG], Q(dc->doveUnsatDiff[tCTG][tCTG]), cc->contUnsatDiff[tCTG][tCTG], R(cc->contUnsatDiff[tCTG][tCTG])); + fprintf(F, "contig-repeat %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tCTG][tRPT], P(dd->doveUnsatDiff[tCTG][tRPT]), dc->doveUnsatDiff[tCTG][tRPT], Q(dc->doveUnsatDiff[tCTG][tRPT]), cc->contUnsatDiff[tCTG][tRPT], R(cc->contUnsatDiff[tCTG][tRPT])); + fprintf(F, "contig-bubble %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tCTG][tBUB], P(dd->doveUnsatDiff[tCTG][tBUB]), dc->doveUnsatDiff[tCTG][tBUB], Q(dc->doveUnsatDiff[tCTG][tBUB]), cc->contUnsatDiff[tCTG][tBUB], R(cc->contUnsatDiff[tCTG][tBUB])); + fprintf(F, "contig-unassembled %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tCTG][tUNA], P(dd->doveUnsatDiff[tCTG][tUNA]), dc->doveUnsatDiff[tCTG][tUNA], Q(dc->doveUnsatDiff[tCTG][tUNA]), cc->contUnsatDiff[tCTG][tUNA], R(cc->contUnsatDiff[tCTG][tUNA])); + fprintf(F, "contig-unused %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tCTG][tUNU], P(dd->doveUnsatDiff[tCTG][tUNU]), dc->doveUnsatDiff[tCTG][tUNU], Q(dc->doveUnsatDiff[tCTG][tUNU]), cc->contUnsatDiff[tCTG][tUNU], R(cc->contUnsatDiff[tCTG][tUNU])); fprintf(F, "\n"); -//fprintf(F, "repeat-contig %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tRPT][tCTG], P(dd->doveUnsatDiff[tRPT][tCTG]), dc->doveUnsatDiff[tRPT][tCTG], Q(dc->doveUnsatDiff[tRPT][tCTG]), cc->contUnsatDiff[tRPT][tCTG], R(cc->contUnsatDiff[tRPT][tCTG])); - fprintf(F, "repeat-repeat %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tRPT][tRPT], P(dd->doveUnsatDiff[tRPT][tRPT]), dc->doveUnsatDiff[tRPT][tRPT], Q(dc->doveUnsatDiff[tRPT][tRPT]), cc->contUnsatDiff[tRPT][tRPT], R(cc->contUnsatDiff[tRPT][tRPT])); - fprintf(F, "repeat-bubble %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tRPT][tBUB], P(dd->doveUnsatDiff[tRPT][tBUB]), dc->doveUnsatDiff[tRPT][tBUB], Q(dc->doveUnsatDiff[tRPT][tBUB]), cc->contUnsatDiff[tRPT][tBUB], R(cc->contUnsatDiff[tRPT][tBUB])); - fprintf(F, "repeat-unassembled %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tRPT][tUNA], P(dd->doveUnsatDiff[tRPT][tUNA]), dc->doveUnsatDiff[tRPT][tUNA], Q(dc->doveUnsatDiff[tRPT][tUNA]), cc->contUnsatDiff[tRPT][tUNA], R(cc->contUnsatDiff[tRPT][tUNA])); - fprintf(F, "repeat-unused %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tRPT][tUNU], P(dd->doveUnsatDiff[tRPT][tUNU]), dc->doveUnsatDiff[tRPT][tUNU], Q(dc->doveUnsatDiff[tRPT][tUNU]), cc->contUnsatDiff[tRPT][tUNU], R(cc->contUnsatDiff[tRPT][tUNU])); +//fprintf(F, "repeat-contig %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tRPT][tCTG], P(dd->doveUnsatDiff[tRPT][tCTG]), dc->doveUnsatDiff[tRPT][tCTG], Q(dc->doveUnsatDiff[tRPT][tCTG]), cc->contUnsatDiff[tRPT][tCTG], R(cc->contUnsatDiff[tRPT][tCTG])); + fprintf(F, "repeat-repeat %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tRPT][tRPT], P(dd->doveUnsatDiff[tRPT][tRPT]), dc->doveUnsatDiff[tRPT][tRPT], Q(dc->doveUnsatDiff[tRPT][tRPT]), cc->contUnsatDiff[tRPT][tRPT], R(cc->contUnsatDiff[tRPT][tRPT])); + fprintf(F, "repeat-bubble %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tRPT][tBUB], P(dd->doveUnsatDiff[tRPT][tBUB]), dc->doveUnsatDiff[tRPT][tBUB], Q(dc->doveUnsatDiff[tRPT][tBUB]), cc->contUnsatDiff[tRPT][tBUB], R(cc->contUnsatDiff[tRPT][tBUB])); + fprintf(F, "repeat-unassembled %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tRPT][tUNA], P(dd->doveUnsatDiff[tRPT][tUNA]), dc->doveUnsatDiff[tRPT][tUNA], Q(dc->doveUnsatDiff[tRPT][tUNA]), cc->contUnsatDiff[tRPT][tUNA], R(cc->contUnsatDiff[tRPT][tUNA])); + fprintf(F, "repeat-unused %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tRPT][tUNU], P(dd->doveUnsatDiff[tRPT][tUNU]), dc->doveUnsatDiff[tRPT][tUNU], Q(dc->doveUnsatDiff[tRPT][tUNU]), cc->contUnsatDiff[tRPT][tUNU], R(cc->contUnsatDiff[tRPT][tUNU])); fprintf(F, "\n"); -//fprintf(F, "bubble-contig %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tBUB][tCTG], P(dd->doveUnsatDiff[tBUB][tCTG]), dc->doveUnsatDiff[tBUB][tCTG], Q(dc->doveUnsatDiff[tBUB][tCTG]), cc->contUnsatDiff[tBUB][tCTG], R(cc->contUnsatDiff[tBUB][tCTG])); -//fprintf(F, "bubble-repeat %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tBUB][tRPT], P(dd->doveUnsatDiff[tBUB][tRPT]), dc->doveUnsatDiff[tBUB][tRPT], Q(dc->doveUnsatDiff[tBUB][tRPT]), cc->contUnsatDiff[tBUB][tRPT], R(cc->contUnsatDiff[tBUB][tRPT])); - fprintf(F, "bubble-bubble %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tBUB][tBUB], P(dd->doveUnsatDiff[tBUB][tBUB]), dc->doveUnsatDiff[tBUB][tBUB], Q(dc->doveUnsatDiff[tBUB][tBUB]), cc->contUnsatDiff[tBUB][tBUB], R(cc->contUnsatDiff[tBUB][tBUB])); - fprintf(F, "bubble-unassembled %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tBUB][tUNA], P(dd->doveUnsatDiff[tBUB][tUNA]), dc->doveUnsatDiff[tBUB][tUNA], Q(dc->doveUnsatDiff[tBUB][tUNA]), cc->contUnsatDiff[tBUB][tUNA], R(cc->contUnsatDiff[tBUB][tUNA])); - fprintf(F, "bubble-unused %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tBUB][tUNU], P(dd->doveUnsatDiff[tBUB][tUNU]), dc->doveUnsatDiff[tBUB][tUNU], Q(dc->doveUnsatDiff[tBUB][tUNU]), cc->contUnsatDiff[tBUB][tUNU], R(cc->contUnsatDiff[tBUB][tUNU])); +//fprintf(F, "bubble-contig %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tBUB][tCTG], P(dd->doveUnsatDiff[tBUB][tCTG]), dc->doveUnsatDiff[tBUB][tCTG], Q(dc->doveUnsatDiff[tBUB][tCTG]), cc->contUnsatDiff[tBUB][tCTG], R(cc->contUnsatDiff[tBUB][tCTG])); +//fprintf(F, "bubble-repeat %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tBUB][tRPT], P(dd->doveUnsatDiff[tBUB][tRPT]), dc->doveUnsatDiff[tBUB][tRPT], Q(dc->doveUnsatDiff[tBUB][tRPT]), cc->contUnsatDiff[tBUB][tRPT], R(cc->contUnsatDiff[tBUB][tRPT])); + fprintf(F, "bubble-bubble %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tBUB][tBUB], P(dd->doveUnsatDiff[tBUB][tBUB]), dc->doveUnsatDiff[tBUB][tBUB], Q(dc->doveUnsatDiff[tBUB][tBUB]), cc->contUnsatDiff[tBUB][tBUB], R(cc->contUnsatDiff[tBUB][tBUB])); + fprintf(F, "bubble-unassembled %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tBUB][tUNA], P(dd->doveUnsatDiff[tBUB][tUNA]), dc->doveUnsatDiff[tBUB][tUNA], Q(dc->doveUnsatDiff[tBUB][tUNA]), cc->contUnsatDiff[tBUB][tUNA], R(cc->contUnsatDiff[tBUB][tUNA])); + fprintf(F, "bubble-unused %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tBUB][tUNU], P(dd->doveUnsatDiff[tBUB][tUNU]), dc->doveUnsatDiff[tBUB][tUNU], Q(dc->doveUnsatDiff[tBUB][tUNU]), cc->contUnsatDiff[tBUB][tUNU], R(cc->contUnsatDiff[tBUB][tUNU])); fprintf(F, "\n"); -//fprintf(F, "unassembled-contig %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tUNA][tCTG], P(dd->doveUnsatDiff[tUNA][tCTG]), dc->doveUnsatDiff[tUNA][tCTG], Q(dc->doveUnsatDiff[tUNA][tCTG]), cc->contUnsatDiff[tUNA][tCTG], R(cc->contUnsatDiff[tUNA][tCTG])); -//fprintf(F, "unassembled-repeat %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tUNA][tRPT], P(dd->doveUnsatDiff[tUNA][tRPT]), dc->doveUnsatDiff[tUNA][tRPT], Q(dc->doveUnsatDiff[tUNA][tRPT]), cc->contUnsatDiff[tUNA][tRPT], R(cc->contUnsatDiff[tUNA][tRPT])); -//fprintf(F, "unassembled-bubble %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tUNA][tBUB], P(dd->doveUnsatDiff[tUNA][tBUB]), dc->doveUnsatDiff[tUNA][tBUB], Q(dc->doveUnsatDiff[tUNA][tBUB]), cc->contUnsatDiff[tUNA][tBUB], R(cc->contUnsatDiff[tUNA][tBUB])); - fprintf(F, "unassembled-unassembled %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tUNA][tUNA], P(dd->doveUnsatDiff[tUNA][tUNA]), dc->doveUnsatDiff[tUNA][tUNA], Q(dc->doveUnsatDiff[tUNA][tUNA]), cc->contUnsatDiff[tUNA][tUNA], R(cc->contUnsatDiff[tUNA][tUNA])); - fprintf(F, "unassembled-unused %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tUNA][tUNU], P(dd->doveUnsatDiff[tUNA][tUNU]), dc->doveUnsatDiff[tUNA][tUNU], Q(dc->doveUnsatDiff[tUNA][tUNU]), cc->contUnsatDiff[tUNA][tUNU], R(cc->contUnsatDiff[tUNA][tUNU])); +//fprintf(F, "unassembled-contig %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tUNA][tCTG], P(dd->doveUnsatDiff[tUNA][tCTG]), dc->doveUnsatDiff[tUNA][tCTG], Q(dc->doveUnsatDiff[tUNA][tCTG]), cc->contUnsatDiff[tUNA][tCTG], R(cc->contUnsatDiff[tUNA][tCTG])); +//fprintf(F, "unassembled-repeat %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tUNA][tRPT], P(dd->doveUnsatDiff[tUNA][tRPT]), dc->doveUnsatDiff[tUNA][tRPT], Q(dc->doveUnsatDiff[tUNA][tRPT]), cc->contUnsatDiff[tUNA][tRPT], R(cc->contUnsatDiff[tUNA][tRPT])); +//fprintf(F, "unassembled-bubble %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tUNA][tBUB], P(dd->doveUnsatDiff[tUNA][tBUB]), dc->doveUnsatDiff[tUNA][tBUB], Q(dc->doveUnsatDiff[tUNA][tBUB]), cc->contUnsatDiff[tUNA][tBUB], R(cc->contUnsatDiff[tUNA][tBUB])); + fprintf(F, "unassembled-unassembled %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tUNA][tUNA], P(dd->doveUnsatDiff[tUNA][tUNA]), dc->doveUnsatDiff[tUNA][tUNA], Q(dc->doveUnsatDiff[tUNA][tUNA]), cc->contUnsatDiff[tUNA][tUNA], R(cc->contUnsatDiff[tUNA][tUNA])); + fprintf(F, "unassembled-unused %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tUNA][tUNU], P(dd->doveUnsatDiff[tUNA][tUNU]), dc->doveUnsatDiff[tUNA][tUNU], Q(dc->doveUnsatDiff[tUNA][tUNU]), cc->contUnsatDiff[tUNA][tUNU], R(cc->contUnsatDiff[tUNA][tUNU])); fprintf(F, "\n"); -//fprintf(F, "unused-contig %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tUNU][tCTG], P(dd->doveUnsatDiff[tUNU][tCTG]), dc->doveUnsatDiff[tUNU][tCTG], Q(dc->doveUnsatDiff[tUNU][tCTG]), cc->contUnsatDiff[tUNU][tCTG], R(cc->contUnsatDiff[tUNU][tCTG])); -//fprintf(F, "unused-repeat %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tUNU][tRPT], P(dd->doveUnsatDiff[tUNU][tRPT]), dc->doveUnsatDiff[tUNU][tRPT], Q(dc->doveUnsatDiff[tUNU][tRPT]), cc->contUnsatDiff[tUNU][tRPT], R(cc->contUnsatDiff[tUNU][tRPT])); -//fprintf(F, "unused-bubble %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tUNU][tBUB], P(dd->doveUnsatDiff[tUNU][tBUB]), dc->doveUnsatDiff[tUNU][tBUB], Q(dc->doveUnsatDiff[tUNU][tBUB]), cc->contUnsatDiff[tUNU][tBUB], R(cc->contUnsatDiff[tUNU][tBUB])); -//fprintf(F, "unused-unassembled %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tUNU][tUNA], P(dd->doveUnsatDiff[tUNU][tUNA]), dc->doveUnsatDiff[tUNU][tUNA], Q(dc->doveUnsatDiff[tUNU][tUNA]), cc->contUnsatDiff[tUNU][tUNA], R(cc->contUnsatDiff[tUNU][tUNA])); - fprintf(F, "unused-unused %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%% %12"F_U64P" %6.2f%%\n", dd->doveUnsatDiff[tUNU][tUNU], P(dd->doveUnsatDiff[tUNU][tUNU]), dc->doveUnsatDiff[tUNU][tUNU], Q(dc->doveUnsatDiff[tUNU][tUNU]), cc->contUnsatDiff[tUNU][tUNU], R(cc->contUnsatDiff[tUNU][tUNU])); +//fprintf(F, "unused-contig %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tUNU][tCTG], P(dd->doveUnsatDiff[tUNU][tCTG]), dc->doveUnsatDiff[tUNU][tCTG], Q(dc->doveUnsatDiff[tUNU][tCTG]), cc->contUnsatDiff[tUNU][tCTG], R(cc->contUnsatDiff[tUNU][tCTG])); +//fprintf(F, "unused-repeat %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tUNU][tRPT], P(dd->doveUnsatDiff[tUNU][tRPT]), dc->doveUnsatDiff[tUNU][tRPT], Q(dc->doveUnsatDiff[tUNU][tRPT]), cc->contUnsatDiff[tUNU][tRPT], R(cc->contUnsatDiff[tUNU][tRPT])); +//fprintf(F, "unused-bubble %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tUNU][tBUB], P(dd->doveUnsatDiff[tUNU][tBUB]), dc->doveUnsatDiff[tUNU][tBUB], Q(dc->doveUnsatDiff[tUNU][tBUB]), cc->contUnsatDiff[tUNU][tBUB], R(cc->contUnsatDiff[tUNU][tBUB])); +//fprintf(F, "unused-unassembled %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tUNU][tUNA], P(dd->doveUnsatDiff[tUNU][tUNA]), dc->doveUnsatDiff[tUNU][tUNA], Q(dc->doveUnsatDiff[tUNU][tUNA]), cc->contUnsatDiff[tUNU][tUNA], R(cc->contUnsatDiff[tUNU][tUNA])); + fprintf(F, "unused-unused %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%% %12" F_U64P " %6.2f%%\n", dd->doveUnsatDiff[tUNU][tUNU], P(dd->doveUnsatDiff[tUNU][tUNU]), dc->doveUnsatDiff[tUNU][tUNU], Q(dc->doveUnsatDiff[tUNU][tUNU]), cc->contUnsatDiff[tUNU][tUNU], R(cc->contUnsatDiff[tUNU][tUNU])); fprintf(F, "\n"); fprintf(F, "\n"); diff --git a/src/bogart/AS_BAT_Logging.C b/src/bogart/AS_BAT_Logging.C index 83dc5c1e3..53c45b537 100644 --- a/src/bogart/AS_BAT_Logging.C +++ b/src/bogart/AS_BAT_Logging.C @@ -228,7 +228,7 @@ writeLog(char const *fmt, ...) { if ((lf->name[0] != 0) && (lf->length > maxLength)) { - fprintf(lf->file, "logFile()-- size "F_U64" exceeds limit of "F_U64"; rotate to new file.\n", + fprintf(lf->file, "logFile()-- size " F_U64 " exceeds limit of " F_U64 "; rotate to new file.\n", lf->length, maxLength); lf->rotate(); } diff --git a/src/bogart/AS_BAT_MarkRepeatReads.C b/src/bogart/AS_BAT_MarkRepeatReads.C index 9962d30d6..5c049b263 100644 --- a/src/bogart/AS_BAT_MarkRepeatReads.C +++ b/src/bogart/AS_BAT_MarkRepeatReads.C @@ -926,7 +926,7 @@ markRepeatReads(AssemblyGraph *AG, uint32 numThreads = omp_get_max_threads(); uint32 blockSize = (tiLimit < 100000 * numThreads) ? numThreads : tiLimit / 99999; - writeLog("repeatDetect()-- working on "F_U32" tigs, with "F_U32" thread%s.\n", tiLimit, numThreads, (numThreads == 1) ? "" : "s"); + writeLog("repeatDetect()-- working on " F_U32 " tigs, with " F_U32 " thread%s.\n", tiLimit, numThreads, (numThreads == 1) ? "" : "s"); vector repeatOlaps; // Overlaps to reads promoted to tig coords diff --git a/src/bogart/AS_BAT_OverlapCache.C b/src/bogart/AS_BAT_OverlapCache.C index 8859e0de2..0a6340892 100644 --- a/src/bogart/AS_BAT_OverlapCache.C +++ b/src/bogart/AS_BAT_OverlapCache.C @@ -97,9 +97,9 @@ getMemorySize(void) { uint64 pageSize = sysconf(_SC_PAGESIZE); uint64 physMemory = physPages * pageSize; - writeStatus("PHYS_PAGES = "F_U64"\n", physPages); - writeStatus("PAGE_SIZE = "F_U64"\n", pageSize); - writeStatus("MEMORY = "F_U64"\n", physMemory); + writeStatus("PHYS_PAGES = " F_U64 "\n", physPages); + writeStatus("PAGE_SIZE = " F_U64 "\n", pageSize); + writeStatus("MEMORY = " F_U64 "\n", physMemory); return(physMemory); } @@ -152,10 +152,10 @@ OverlapCache::OverlapCache(ovStore *ovlStoreUniq, if (memlimit == UINT64_MAX) { _memLimit = getMemorySize(); - writeStatus("OverlapCache()-- limited to "F_U64"MB memory (total physical memory).\n", _memLimit >> 20); + writeStatus("OverlapCache()-- limited to " F_U64 "MB memory (total physical memory).\n", _memLimit >> 20); } else if (memlimit > 0) { _memLimit = memlimit; - writeStatus("OverlapCache()-- limited to "F_U64"MB memory (user supplied).\n", _memLimit >> 20); + writeStatus("OverlapCache()-- limited to " F_U64 "MB memory (user supplied).\n", _memLimit >> 20); } else { writeStatus("OverlapCache()-- using unlimited memory (-M 0).\n"); _memLimit = UINT64_MAX; @@ -196,24 +196,24 @@ OverlapCache::OverlapCache(ovStore *ovlStoreUniq, memTT = memFI + memBE + memUL + memUT + memID + memOS + memC1 + memC2 + memC3 + memC4; } - writeStatus("OverlapCache()-- %7"F_U64P"MB for read data.\n", memFI >> 20); - writeStatus("OverlapCache()-- %7"F_U64P"MB for best edges.\n", memBE >> 20); - writeStatus("OverlapCache()-- %7"F_U64P"MB for unitig layouts.\n", memUL >> 20); - writeStatus("OverlapCache()-- %7"F_U64P"MB for tigs.\n", memUT >> 20); - writeStatus("OverlapCache()-- %7"F_U64P"MB for id maps.\n", memID >> 20); - writeStatus("OverlapCache()-- %7"F_U64P"MB for error profiles.\n", memEP >> 20); - writeStatus("OverlapCache()-- %7"F_U64P"MB for overlap cache pointers.\n", memC1 >> 20); - writeStatus("OverlapCache()-- %7"F_U64P"MB for overlap cache initial bucket.\n", memC2 >> 20); - writeStatus("OverlapCache()-- %7"F_U64P"MB for overlap cache thread data.\n", memC3 >> 20); - writeStatus("OverlapCache()-- %7"F_U64P"MB for number of overlaps per read.\n", memC4 >> 20); - writeStatus("OverlapCache()-- %7"F_U64P"MB for other processes.\n", memOS >> 20); + writeStatus("OverlapCache()-- %7" F_U64P "MB for read data.\n", memFI >> 20); + writeStatus("OverlapCache()-- %7" F_U64P "MB for best edges.\n", memBE >> 20); + writeStatus("OverlapCache()-- %7" F_U64P "MB for unitig layouts.\n", memUL >> 20); + writeStatus("OverlapCache()-- %7" F_U64P "MB for tigs.\n", memUT >> 20); + writeStatus("OverlapCache()-- %7" F_U64P "MB for id maps.\n", memID >> 20); + writeStatus("OverlapCache()-- %7" F_U64P "MB for error profiles.\n", memEP >> 20); + writeStatus("OverlapCache()-- %7" F_U64P "MB for overlap cache pointers.\n", memC1 >> 20); + writeStatus("OverlapCache()-- %7" F_U64P "MB for overlap cache initial bucket.\n", memC2 >> 20); + writeStatus("OverlapCache()-- %7" F_U64P "MB for overlap cache thread data.\n", memC3 >> 20); + writeStatus("OverlapCache()-- %7" F_U64P "MB for number of overlaps per read.\n", memC4 >> 20); + writeStatus("OverlapCache()-- %7" F_U64P "MB for other processes.\n", memOS >> 20); writeStatus("OverlapCache()-- ---------\n"); - writeStatus("OverlapCache()-- %7"F_U64P"MB for data structures (sum of above).\n", memTT >> 20); + writeStatus("OverlapCache()-- %7" F_U64P "MB for data structures (sum of above).\n", memTT >> 20); if (_memLimit <= memTT) { int64 defecit = (int64)memTT - (int64)_memLimit; - writeStatus("OverlapCache()-- %7"F_S64P"MB available for overlaps.\n", defecit); + writeStatus("OverlapCache()-- %7" F_S64P "MB available for overlaps.\n", defecit); writeStatus("OverlapCache()-- Out of memory before loading overlaps; increase -M.\n"); exit(1); } @@ -221,7 +221,7 @@ OverlapCache::OverlapCache(ovStore *ovlStoreUniq, _memLimit -= memTT; _memUsed = 0; - writeStatus("OverlapCache()-- %7"F_U64P"MB available for overlaps.\n", _memLimit >> 20); + writeStatus("OverlapCache()-- %7" F_U64P "MB available for overlaps.\n", _memLimit >> 20); writeStatus("\n"); // Decide on the default block size. We want to use large blocks (to reduce the number of @@ -330,7 +330,7 @@ OverlapCache::computeOverlapLimit(void) { if (_maxPer < UINT32_MAX) { // -N supplied on the command line, use that instead. - writeStatus("OverlapCache()-- _maxPer = "F_U32" overlaps/read (from command line)\n", _maxPer); + writeStatus("OverlapCache()-- _maxPer = " F_U32 " overlaps/read (from command line)\n", _maxPer); return; } @@ -354,11 +354,11 @@ OverlapCache::computeOverlapLimit(void) { _maxPer = (_memLimit - _memUsed) / (RI->numReads() * sizeof(BAToverlap)); - writeStatus("OverlapCache()-- Initial guess at _maxPer="F_U32" (max of "F_U32") from (memLimit="F_U64" - memUsed="F_U64") / (numReads="F_U32" * sizeof(OVL)="F_SIZE_T")\n", + writeStatus("OverlapCache()-- Initial guess at _maxPer=" F_U32 " (max of " F_U32 ") from (memLimit=" F_U64 " - memUsed=" F_U64 ") / (numReads=" F_U32 " * sizeof(OVL)=" F_SIZE_T ")\n", _maxPer, numPerMax, _memLimit, _memUsed, RI->numReads(), sizeof(BAToverlap)); if (_maxPer < 10) - writeStatus("OverlapCache()-- ERROR: not enough memory to load overlaps (_maxPer="F_U32" < 10).\n", _maxPer), exit(1); + writeStatus("OverlapCache()-- ERROR: not enough memory to load overlaps (_maxPer=" F_U32 " < 10).\n", _maxPer), exit(1); uint64 totalLoad = 0; // Total overlaps we would load at this threshold @@ -394,7 +394,7 @@ OverlapCache::computeOverlapLimit(void) { } } - writeStatus("OverlapCache()-- _maxPer=%7"F_U32P" (numBelow="F_U32" numEqual="F_U32" numAbove="F_U32" totalLoad="F_U64" -- "F_U64" + "F_U64" = "F_U64" > 20, adjust); @@ -446,25 +446,25 @@ OverlapCache::computeOverlapLimit(void) { } } - writeStatus("OverlapCache()-- _maxPer=%7"F_U32P" (overestimated, revert to last good and stop)\n", _maxPer); + writeStatus("OverlapCache()-- _maxPer=%7" F_U32P " (overestimated, revert to last good and stop)\n", _maxPer); } } // Report writeStatus("\n"); - writeStatus("OverlapCache()-- blockSize = "F_U32" ("F_SIZE_T"MB)\n", _storMax, (_storMax * sizeof(BAToverlap)) >> 20); + writeStatus("OverlapCache()-- blockSize = " F_U32 " (" F_SIZE_T "MB)\n", _storMax, (_storMax * sizeof(BAToverlap)) >> 20); writeStatus("\n"); - writeStatus("OverlapCache()-- _maxPer = "F_U32" overlaps/reads\n", _maxPer); - writeStatus("OverlapCache()-- numBelow = "F_U32" reads (all overlaps loaded)\n", numBelow); - writeStatus("OverlapCache()-- numEqual = "F_U32" reads (all overlaps loaded)\n", numEqual); - writeStatus("OverlapCache()-- numAbove = "F_U32" reads (some overlaps loaded)\n", numAbove); - writeStatus("OverlapCache()-- totalLoad = "F_U64" overlaps (%6.2f%%)\n", totalLoad, 100.0 * totalLoad / _ovlStoreUniq->numOverlapsInRange()); + writeStatus("OverlapCache()-- _maxPer = " F_U32 " overlaps/reads\n", _maxPer); + writeStatus("OverlapCache()-- numBelow = " F_U32 " reads (all overlaps loaded)\n", numBelow); + writeStatus("OverlapCache()-- numEqual = " F_U32 " reads (all overlaps loaded)\n", numEqual); + writeStatus("OverlapCache()-- numAbove = " F_U32 " reads (some overlaps loaded)\n", numAbove); + writeStatus("OverlapCache()-- totalLoad = " F_U64 " overlaps (%6.2f%%)\n", totalLoad, 100.0 * totalLoad / _ovlStoreUniq->numOverlapsInRange()); writeStatus("\n"); - writeStatus("OverlapCache()-- availForOverlaps = "F_U64"MB\n", _memLimit >> 20); - writeStatus("OverlapCache()-- totalMemory = "F_U64"MB for organization\n", _memUsed >> 20); - writeStatus("OverlapCache()-- totalMemory = "F_U64"MB for overlaps\n", (totalLoad * sizeof(BAToverlap)) >> 20); - writeStatus("OverlapCache()-- totalMemory = "F_U64"MB used\n", (_memUsed + totalLoad * sizeof(BAToverlap)) >> 20); + writeStatus("OverlapCache()-- availForOverlaps = " F_U64 "MB\n", _memLimit >> 20); + writeStatus("OverlapCache()-- totalMemory = " F_U64 "MB for organization\n", _memUsed >> 20); + writeStatus("OverlapCache()-- totalMemory = " F_U64 "MB for overlaps\n", (totalLoad * sizeof(BAToverlap)) >> 20); + writeStatus("OverlapCache()-- totalMemory = " F_U64 "MB used\n", (_memUsed + totalLoad * sizeof(BAToverlap)) >> 20); writeStatus("\n"); delete [] numPer; @@ -588,7 +588,7 @@ OverlapCache::filterOverlaps(uint32 maxEvalue, uint32 minOverlap, uint32 no) { ns++; if (ns > _maxPer) - writeStatus("WARNING: read "F_U32" loaded "F_U32" overlas (it has "F_U32" in total); over the limit of "F_U32"\n", + writeStatus("WARNING: read " F_U32 " loaded " F_U32 " overlas (it has " F_U32 " in total); over the limit of " F_U32 "\n", _ovs[0].a_iid, ns, no, _maxPer); return(ns); @@ -710,7 +710,7 @@ OverlapCache::loadOverlaps(double erate, uint32 minOverlap, const char *prefix, assert(storEnd == _storLen); if ((numReads++ % 1000000) == 0) - writeStatus("OverlapCache()-- Loading: overlaps processed %12"F_U64P" (%06.2f%%) loaded %12"F_U64P" (%06.2f%%) droppeddupe %12"F_U64P" (%06.2f%%) (at read iid %d)\n", + writeStatus("OverlapCache()-- Loading: overlaps processed %12" F_U64P " (%06.2f%%) loaded %12" F_U64P " (%06.2f%%) droppeddupe %12" F_U64P " (%06.2f%%) (at read iid %d)\n", numTotal, 100.0 * numTotal / numStore, numLoaded, 100.0 * numLoaded / numStore, numDups, 100.0 * numDups / numStore, @@ -725,7 +725,7 @@ OverlapCache::loadOverlaps(double erate, uint32 minOverlap, const char *prefix, if (ovlDat) fclose(ovlDat); - writeStatus("OverlapCache()-- Loading: overlaps processed %12"F_U64P" (%06.2f%%) loaded %12"F_U64P" (%06.2f%%) droppeddupe %12"F_U64P" (%06.2f%%)\n", + writeStatus("OverlapCache()-- Loading: overlaps processed %12" F_U64P " (%06.2f%%) loaded %12" F_U64P " (%06.2f%%) droppeddupe %12" F_U64P " (%06.2f%%)\n", numTotal, 100.0 * numTotal / numStore, numLoaded, 100.0 * numLoaded / numStore, numDups, 100.0 * numDups / numStore); @@ -796,9 +796,9 @@ OverlapCache::removeWeakOverlaps(uint32 *minEvalue5p, } } - writeLog("OverlapCache::removeWeakOverlaps()-- removed "F_U64" weak overlaps.\n", removed); - writeLog("OverlapCache::removeWeakOverlaps()-- ignored "F_U64" contained overlaps.\n", ignored); - writeLog("OverlapCache::removeWeakOverlaps()-- retained "F_U64" strong overlaps.\n", saved); + writeLog("OverlapCache::removeWeakOverlaps()-- removed " F_U64 " weak overlaps.\n", removed); + writeLog("OverlapCache::removeWeakOverlaps()-- ignored " F_U64 " contained overlaps.\n", ignored); + writeLog("OverlapCache::removeWeakOverlaps()-- retained " F_U64 " strong overlaps.\n", saved); } @@ -907,7 +907,7 @@ OverlapCache::load(const char *prefix, double erate) { // For each read, remove any overlaps to deleted reads. - writeLog("OverlapCache()-- Loaded "F_U64" overlaps.\n", nOvl); + writeLog("OverlapCache()-- Loaded " F_U64 " overlaps.\n", nOvl); if (doCleaning) { uint64 nDel = 0; @@ -929,7 +929,7 @@ OverlapCache::load(const char *prefix, double erate) { if ((RI->readLength(fi) == 0) && (_cacheLen[fi] > 0)) { nDel++; - fprintf(F, "Removing "F_U32" overlaps from deleted deleted read "F_U32"\n", _cacheLen[fi], fi); + fprintf(F, "Removing " F_U32 " overlaps from deleted deleted read " F_U32 "\n", _cacheLen[fi], fi); _cachePtr[fi] = NULL; _cacheLen[fi] = 0; } @@ -951,7 +951,7 @@ OverlapCache::load(const char *prefix, double erate) { if (_cacheLen[fi] != on) { nMod++; nOvl += _cacheLen[fi] - on; - fprintf(F, "Removing "F_U32" overlaps from living read "F_U32"\n", _cacheLen[fi] - on, fi); + fprintf(F, "Removing " F_U32 " overlaps from living read " F_U32 "\n", _cacheLen[fi] - on, fi); memset(_cachePtr[fi] + on, 0xff, (_cacheLen[fi] - on) * (sizeof(BAToverlap))); } @@ -960,7 +960,7 @@ OverlapCache::load(const char *prefix, double erate) { fclose(F); - writeStatus("OverlapCache()-- Removed all overlaps from "F_U64" deleted reads. Removed "F_U64" overlaps from "F_U64" alive reads.\n", + writeStatus("OverlapCache()-- Removed all overlaps from " F_U64 " deleted reads. Removed " F_U64 " overlaps from " F_U64 " alive reads.\n", nDel, nOvl, nMod); } diff --git a/src/bogart/AS_BAT_PopBubbles.C b/src/bogart/AS_BAT_PopBubbles.C index 6e0594481..71cad13ad 100644 --- a/src/bogart/AS_BAT_PopBubbles.C +++ b/src/bogart/AS_BAT_PopBubbles.C @@ -85,7 +85,7 @@ findPotentialBubbles(TigVector &tigs, uint32 tiBlockSize = (tiLimit < 100000 * tiNumThreads) ? tiNumThreads : tiLimit / 99999; writeStatus("\n"); - writeStatus("bubbleDetect()-- working on "F_U32" tigs, with "F_U32" thread%s.\n", tiLimit, tiNumThreads, (tiNumThreads == 1) ? "" : "s"); + writeStatus("bubbleDetect()-- working on " F_U32 " tigs, with " F_U32 " thread%s.\n", tiLimit, tiNumThreads, (tiNumThreads == 1) ? "" : "s"); for (uint32 ti=0; ti *placed = findBubbleReadPlacements(tigs, potentialBubbles, deviationBubble); @@ -746,7 +746,7 @@ popBubbles(TigVector &tigs, if ((nt == nReads) || ((n5 > 0) && (n3 > 0))) - writeLog("tig %8u length %9u -> target %8u piece %2u position %9u-%-9u length %8u - expected %3"F_SIZE_TP" reads, had %3"F_SIZE_TP" reads. n5=%3u n3=%3u nt=%3u\n", + writeLog("tig %8u length %9u -> target %8u piece %2u position %9u-%-9u length %8u - expected %3" F_SIZE_TP " reads, had %3" F_SIZE_TP " reads. n5=%3u n3=%3u nt=%3u\n", bubble->id(), bubble->getLength(), targets[tt]->target->id(), tt, targets[tt]->bgn, targets[tt]->end, targets[tt]->end - targets[tt]->bgn, tigReads.size(), diff --git a/src/bogart/AS_BAT_PromoteToSingleton.C b/src/bogart/AS_BAT_PromoteToSingleton.C index 2d915d6aa..ecf39e5fb 100644 --- a/src/bogart/AS_BAT_PromoteToSingleton.C +++ b/src/bogart/AS_BAT_PromoteToSingleton.C @@ -70,6 +70,6 @@ promoteToSingleton(TigVector &tigs) { utg->addRead(read, 0, false); } - writeStatus("promoteToSingleton()-- Moved "F_U32" unplaced read%s to singleton tigs.\n", + writeStatus("promoteToSingleton()-- Moved " F_U32 " unplaced read%s to singleton tigs.\n", nPromoted, (nPromoted == 1) ? "" : "s"); } diff --git a/src/bogart/AS_BAT_ReadInfo.C b/src/bogart/AS_BAT_ReadInfo.C index 0fc8661cd..ad967b592 100644 --- a/src/bogart/AS_BAT_ReadInfo.C +++ b/src/bogart/AS_BAT_ReadInfo.C @@ -76,7 +76,7 @@ ReadInfo::ReadInfo(gkStore *gkp, } if (minReadLen > 0) - writeStatus("ReadInfo()-- Using %d reads, ignoring %u reads less than "F_U32" bp long.\n", + writeStatus("ReadInfo()-- Using %d reads, ignoring %u reads less than " F_U32 " bp long.\n", numLoaded, numSkipped, minReadLen); else writeStatus("ReadInfo()-- Using %d reads, no minimum read length used.\n", diff --git a/src/bogart/AS_BAT_ReadInfo.H b/src/bogart/AS_BAT_ReadInfo.H index 6f2da36f4..f79703c91 100644 --- a/src/bogart/AS_BAT_ReadInfo.H +++ b/src/bogart/AS_BAT_ReadInfo.H @@ -83,9 +83,9 @@ public: } if ((aovl <= 0) || (bovl <= 0) || (aovl > alen) || (bovl > blen)) { - fprintf(stderr, "WARNING: bogus overlap found for A="F_U32" B="F_U32"\n", a_iid, b_iid); - fprintf(stderr, "WARNING: A len="F_S32" hang="F_S32" ovl="F_S32"\n", alen, a_hang, aovl); - fprintf(stderr, "WARNING: B len="F_S32" hang="F_S32" ovl="F_S32"\n", blen, b_hang, bovl); + fprintf(stderr, "WARNING: bogus overlap found for A=" F_U32 " B=" F_U32 "\n", a_iid, b_iid); + fprintf(stderr, "WARNING: A len=" F_S32 " hang=" F_S32 " ovl=" F_S32 "\n", alen, a_hang, aovl); + fprintf(stderr, "WARNING: B len=" F_S32 " hang=" F_S32 " ovl=" F_S32 "\n", blen, b_hang, bovl); } if (aovl < 0) aovl = 0; diff --git a/src/bogart/AS_BAT_SplitDiscontinuous.C b/src/bogart/AS_BAT_SplitDiscontinuous.C index 583e02b33..79c2c80b4 100644 --- a/src/bogart/AS_BAT_SplitDiscontinuous.C +++ b/src/bogart/AS_BAT_SplitDiscontinuous.C @@ -49,7 +49,7 @@ makeNewUnitig(TigVector &tigs, Unitig *dangler = tigs.newUnitig(false); if (logFileFlagSet(LOG_SPLIT_DISCONTINUOUS)) - writeLog("splitDiscontinuous()-- new tig "F_U32" with "F_U32" reads (starting at read "F_U32").\n", + writeLog("splitDiscontinuous()-- new tig " F_U32 " with " F_U32 " reads (starting at read " F_U32 ").\n", dangler->id(), splitReadsLen, splitReads[0].ident); int splitOffset = -MIN(splitReads[0].position.bgn, splitReads[0].position.end); @@ -95,7 +95,7 @@ void splitDiscontinuous(TigVector &tigs, uint32 minOverlap) { if (minPos == 0) continue; - writeLog("splitDiscontinuous()-- tig "F_U32" offset messed up; reset by "F_S32".\n", tig->id(), minPos); + writeLog("splitDiscontinuous()-- tig " F_U32 " offset messed up; reset by " F_S32 ".\n", tig->id(), minPos); for (uint32 fi=0; fiufpath.size(); fi++) { ufNode *frg = &tig->ufpath[fi]; @@ -148,7 +148,7 @@ void splitDiscontinuous(TigVector &tigs, uint32 minOverlap) { maxEnd = 0; if (logFileFlagSet(LOG_SPLIT_DISCONTINUOUS)) - writeLog("splitDiscontinuous()-- discontinuous tig "F_U32" with "F_SIZE_T" reads broken into:\n", + writeLog("splitDiscontinuous()-- discontinuous tig " F_U32 " with " F_SIZE_T " reads broken into:\n", tig->id(), tig->ufpath.size()); for (uint32 fi=0; fiufpath.size(); fi++) { @@ -198,10 +198,10 @@ void splitDiscontinuous(TigVector &tigs, uint32 minOverlap) { delete [] splitReads; if (numSplit == 0) - writeStatus("splitDiscontinuous()-- Tested "F_U32" tig%s, split none.\n", + writeStatus("splitDiscontinuous()-- Tested " F_U32 " tig%s, split none.\n", numTested, (numTested == 1) ? "" : "s"); else - writeStatus("splitDiscontinuous()-- Tested "F_U32" tig%s, split "F_U32" tig%s into "F_U32" new tig%s.\n", + writeStatus("splitDiscontinuous()-- Tested " F_U32 " tig%s, split " F_U32 " tig%s into " F_U32 " new tig%s.\n", numTested, (numTested == 1) ? "" : "s", numSplit, (numSplit == 1) ? "" : "s", numCreated, (numCreated == 1) ? "" : "s"); diff --git a/src/bogart/AS_BAT_TigVector.C b/src/bogart/AS_BAT_TigVector.C index e3c06da66..4b33eea76 100644 --- a/src/bogart/AS_BAT_TigVector.C +++ b/src/bogart/AS_BAT_TigVector.C @@ -136,10 +136,10 @@ Unitig *&operator[](uint32 i) { if (((i >= _totalTigs)) || ((idx >= _numBlocks)) || (((pos >= _blockNext) && (idx >= _numBlocks - 1)))) { - writeStatus("TigVector::operator[]()-- i="F_U32" with totalTigs="F_U64"\n", i, _totalTigs); - writeStatus("TigVector::operator[]()-- blockSize="F_U64"\n", _blockSize); - writeStatus("TigVector::operator[]()-- idx="F_U32" numBlocks="F_U64"\n", idx, _numBlocks); - writeStatus("TigVector::operator[]()-- pos="F_U32" blockNext="F_U64"\n", pos, _blockNext); + writeStatus("TigVector::operator[]()-- i=" F_U32 " with totalTigs=" F_U64 "\n", i, _totalTigs); + writeStatus("TigVector::operator[]()-- blockSize=" F_U64 "\n", _blockSize); + writeStatus("TigVector::operator[]()-- idx=" F_U32 " numBlocks=" F_U64 "\n", idx, _numBlocks); + writeStatus("TigVector::operator[]()-- pos=" F_U32 " blockNext=" F_U64 "\n", pos, _blockNext); } assert(i < _totalTigs); assert((idx < _numBlocks)); diff --git a/src/bogart/AS_BAT_Unitig.C b/src/bogart/AS_BAT_Unitig.C index f7eb217c7..d63ce671e 100644 --- a/src/bogart/AS_BAT_Unitig.C +++ b/src/bogart/AS_BAT_Unitig.C @@ -137,7 +137,7 @@ void Unitig::computeErrorProfile(const char *UNUSED(prefix), const char *UNUSED(label)) { #ifdef SHOW_PROFILE_CONSTRUCTION - writeLog("errorProfile()-- Find error profile for tig "F_U32" of length "F_U32" with "F_SIZE_T" reads.\n", + writeLog("errorProfile()-- Find error profile for tig " F_U32 " of length " F_U32 " with " F_SIZE_T " reads.\n", id(), getLength(), ufpath.size()); #endif @@ -215,7 +215,7 @@ Unitig::computeErrorProfile(const char *UNUSED(prefix), const char *UNUSED(label #ifdef SHOW_PROFILE_CONSTRUCTION - writeLog("errorProfile()-- tig %u generated "F_SIZE_T" profile regions from "F_SIZE_T" overlaps.\n", id(), errorProfile.size(), olaps.size()); + writeLog("errorProfile()-- tig %u generated " F_SIZE_T " profile regions from " F_SIZE_T " overlaps.\n", id(), errorProfile.size(), olaps.size()); #endif // Walk both lists, adding positive erates and removing negative erates. @@ -309,7 +309,7 @@ Unitig::computeErrorProfile(const char *UNUSED(prefix), const char *UNUSED(label - //writeLog("errorProfile()-- tig %u generated "F_SIZE_T" profile regions with "F_U64" overlap pieces.\n", + //writeLog("errorProfile()-- tig %u generated " F_SIZE_T " profile regions with " F_U64 " overlap pieces.\n", // id(), errorProfile.size(), nPieces); } @@ -363,7 +363,7 @@ Unitig::overlapConsistentWithTig(double deviations, uint32 pbi = bgn / 1000; if (errorProfileIndex.size() <= pbi) - fprintf(stderr, "errorProfileIndex.size() = "F_SIZE_T"\n", errorProfileIndex.size()); + fprintf(stderr, "errorProfileIndex.size() = " F_SIZE_T "\n", errorProfileIndex.size()); assert(pbi < errorProfileIndex.size()); while ((0 < pbi) && (errorProfile[errorProfileIndex[pbi]].bgn > bgn)) { diff --git a/src/bogart/addReadsToUnitigs.C b/src/bogart/addReadsToUnitigs.C index 5b7bc9fce..31ac157e3 100644 --- a/src/bogart/addReadsToUnitigs.C +++ b/src/bogart/addReadsToUnitigs.C @@ -251,7 +251,7 @@ main(int argc, char **argv) { fgets(LL, 1024, LF); } - fprintf(stderr, "Loaded "F_SIZE_T" name to IIDs\n", lookupIID.size()); + fprintf(stderr, "Loaded " F_SIZE_T " name to IIDs\n", lookupIID.size()); } diff --git a/src/bogart/analyzeBest.C b/src/bogart/analyzeBest.C index aab67c61d..53121b7a2 100644 --- a/src/bogart/analyzeBest.C +++ b/src/bogart/analyzeBest.C @@ -189,7 +189,7 @@ main(int argc, char **argv) { for (uint32 i=0; igkStore_getLibrary(i)->libraryName, readPerLib[i], diff --git a/src/bogart/buildGraph.C b/src/bogart/buildGraph.C index 12a324e75..7ee59b88d 100644 --- a/src/bogart/buildGraph.C +++ b/src/bogart/buildGraph.C @@ -142,7 +142,7 @@ loadEdges(char *edgeName, vector &edges, set &vertices) { fgets(edgeLine, 1024, edgeFile); } - fprintf(stderr, "Loaded "F_SIZE_T" edges from '%s'.\n", edges.size(), edgeName); + fprintf(stderr, "Loaded " F_SIZE_T " edges from '%s'.\n", edges.size(), edgeName); } diff --git a/src/bogus/bogus.C b/src/bogus/bogus.C index 67afd3457..2a0e67632 100644 --- a/src/bogus/bogus.C +++ b/src/bogus/bogus.C @@ -645,14 +645,14 @@ main(int argc, char **argv) { //assert(refcnt != 0); if ((refcnt > 0) && (minFrags <= refcnt) && (minLength <= refend - refbgn)) { - fprintf(intervalOutput, "%s\t%8"F_S64P"\t%8"F_S64P"\tREPT\t"F_S64"%s\n", + fprintf(intervalOutput, "%s\t%8" F_S64P "\t%8" F_S64P "\tREPT\t" F_S64 "%s\n", refhdr, refbgn, refend, refcnt, (REPTvalid[ir]) ? "" : " weak"); if (REPTvalid[ir]) - fprintf(gffOutput, "%s\t.\tbogus_rept_interval\t"F_S64"\t"F_S64"\t.\t.\t.\tID=REPT%04d;fragCount="F_S64"\n", + fprintf(gffOutput, "%s\t.\tbogus_rept_interval\t" F_S64 "\t" F_S64 "\t.\t.\t.\tID=REPT%04d;fragCount=" F_S64 "\n", refhdr, refbgn, refend, ir, refcnt); else - fprintf(gffOutput, "%s\t.\tbogus_weak_interval\t"F_S64"\t"F_S64"\t.\t.\t.\tParent=UNIQ%04d;fragCount="F_S64"\n", + fprintf(gffOutput, "%s\t.\tbogus_weak_interval\t" F_S64 "\t" F_S64 "\t.\t.\t.\tParent=UNIQ%04d;fragCount=" F_S64 "\n", refhdr, refbgn, refend, REPTvalidParent[ir], refcnt); } @@ -684,14 +684,14 @@ main(int argc, char **argv) { //assert(refcnt != 0); if ((refcnt > 0) && (minFrags <= refcnt) && (minLength <= refend - refbgn)) { - fprintf(intervalOutput, "%s\t%8"F_S64P"\t%8"F_S64P"\tUNIQ\t"F_S64"%s\n", + fprintf(intervalOutput, "%s\t%8" F_S64P "\t%8" F_S64P "\tUNIQ\t" F_S64 "%s\n", refhdr, refbgn, refend, refcnt, (UNIQvalid[iu]) ? "" : " separation"); if (UNIQvalid[iu]) - fprintf(gffOutput, "%s\t.\tbogus_uniq_interval\t"F_S64"\t"F_S64"\t.\t.\t.\tID=UNIQ%04d;fragCount="F_S64"\n", + fprintf(gffOutput, "%s\t.\tbogus_uniq_interval\t" F_S64 "\t" F_S64 "\t.\t.\t.\tID=UNIQ%04d;fragCount=" F_S64 "\n", refhdr, refbgn, refend, iu, refcnt); else - fprintf(gffOutput, "%s\t.\tbogus_sepr_interval\t"F_S64"\t"F_S64"\t.\t.\t.\tParent=REPT%04d;fragCount="F_S64"\n", + fprintf(gffOutput, "%s\t.\tbogus_sepr_interval\t" F_S64 "\t" F_S64 "\t.\t.\t.\tParent=REPT%04d;fragCount=" F_S64 "\n", refhdr, refbgn, refend, UNIQvalidParent[iu], refcnt); } diff --git a/src/correction/filterCorrectionOverlaps.C b/src/correction/filterCorrectionOverlaps.C index dedb2702a..7b431ef15 100644 --- a/src/correction/filterCorrectionOverlaps.C +++ b/src/correction/filterCorrectionOverlaps.C @@ -360,8 +360,8 @@ main(int argc, char **argv) { fprintf(statsFile, "PARAMETERS:\n"); fprintf(statsFile, "----------\n"); fprintf(statsFile, "\n"); - fprintf(statsFile, "%7"F_U32P" (expected coverage)\n", expectedCoverage); - fprintf(statsFile, "%7"F_U32P" (don't use overlaps shorter than this)\n", minOvlLength); + fprintf(statsFile, "%7" F_U32P " (expected coverage)\n", expectedCoverage); + fprintf(statsFile, "%7" F_U32P " (don't use overlaps shorter than this)\n", minOvlLength); fprintf(statsFile, "%7.3f (don't use overlaps with erate less than this)\n", minErate); fprintf(statsFile, "%7.3f (don't use overlaps with erate more than this)\n", maxErate); fprintf(statsFile, "\n"); @@ -370,32 +370,32 @@ main(int argc, char **argv) { fprintf(statsFile, "\n"); fprintf(statsFile, "IGNORED:\n"); fprintf(statsFile, "\n"); - fprintf(statsFile, "%12"F_U64P" (< %6.4f fraction error)\n", lowErate, AS_OVS_decodeEvalue(minEvalue)); - fprintf(statsFile, "%12"F_U64P" (> %6.4f fraction error)\n", highErate, AS_OVS_decodeEvalue(maxEvalue)); - fprintf(statsFile, "%12"F_U64P" (< %u bases long)\n", tooShort, minOvlLength); - fprintf(statsFile, "%12"F_U64P" (> %u bases long)\n", tooLong, maxOvlLength); + fprintf(statsFile, "%12" F_U64P " (< %6.4f fraction error)\n", lowErate, AS_OVS_decodeEvalue(minEvalue)); + fprintf(statsFile, "%12" F_U64P " (> %6.4f fraction error)\n", highErate, AS_OVS_decodeEvalue(maxEvalue)); + fprintf(statsFile, "%12" F_U64P " (< %u bases long)\n", tooShort, minOvlLength); + fprintf(statsFile, "%12" F_U64P " (> %u bases long)\n", tooLong, maxOvlLength); fprintf(statsFile, "\n"); fprintf(statsFile, "FILTERED:\n"); fprintf(statsFile, "\n"); - fprintf(statsFile, "%12"F_U64P" (too many overlaps, discard these shortest ones)\n", belowCutoff); + fprintf(statsFile, "%12" F_U64P " (too many overlaps, discard these shortest ones)\n", belowCutoff); fprintf(statsFile, "\n"); fprintf(statsFile, "EVIDENCE:\n"); fprintf(statsFile, "\n"); - fprintf(statsFile, "%12"F_U64P" (longest overlaps)\n", retained); + fprintf(statsFile, "%12" F_U64P " (longest overlaps)\n", retained); fprintf(statsFile, "\n"); fprintf(statsFile, "TOTAL:\n"); fprintf(statsFile, "\n"); - fprintf(statsFile, "%12"F_U64P" (all overlaps)\n", totalOverlaps); + fprintf(statsFile, "%12" F_U64P " (all overlaps)\n", totalOverlaps); fprintf(statsFile, "\n"); fprintf(statsFile, "READS:\n"); fprintf(statsFile, "-----\n"); fprintf(statsFile, "\n"); - fprintf(statsFile, "%12"F_U64P" (no overlaps)\n", readsNoOlaps); - fprintf(statsFile, "%12"F_U64P" (no overlaps filtered)\n", reads00OlapsFiltered); - fprintf(statsFile, "%12"F_U64P" (< 50%% overlaps filtered)\n", reads50OlapsFiltered); - fprintf(statsFile, "%12"F_U64P" (< 80%% overlaps filtered)\n", reads80OlapsFiltered); - fprintf(statsFile, "%12"F_U64P" (< 95%% overlaps filtered)\n", reads95OlapsFiltered); - fprintf(statsFile, "%12"F_U64P" (< 100%% overlaps filtered)\n", reads99OlapsFiltered); + fprintf(statsFile, "%12" F_U64P " (no overlaps)\n", readsNoOlaps); + fprintf(statsFile, "%12" F_U64P " (no overlaps filtered)\n", reads00OlapsFiltered); + fprintf(statsFile, "%12" F_U64P " (< 50%% overlaps filtered)\n", reads50OlapsFiltered); + fprintf(statsFile, "%12" F_U64P " (< 80%% overlaps filtered)\n", reads80OlapsFiltered); + fprintf(statsFile, "%12" F_U64P " (< 95%% overlaps filtered)\n", reads95OlapsFiltered); + fprintf(statsFile, "%12" F_U64P " (< 100%% overlaps filtered)\n", reads99OlapsFiltered); fprintf(statsFile, "\n"); fclose(statsFile); diff --git a/src/correction/generateCorrectionLayouts.C b/src/correction/generateCorrectionLayouts.C index 7166d156f..dc04c6ac4 100644 --- a/src/correction/generateCorrectionLayouts.C +++ b/src/correction/generateCorrectionLayouts.C @@ -83,7 +83,7 @@ generateLayout(gkStore *gkpStore, resizeArray(layout->_children, layout->_childrenLen, layout->_childrenMax, ovlLen, resizeArray_doNothing); if (flgFile) - fprintf(flgFile, "Generate layout for read "F_U32" length "F_U32" using up to "F_U32" overlaps.\n", + fprintf(flgFile, "Generate layout for read " F_U32 " length " F_U32 " using up to " F_U32 " overlaps.\n", layout->_tigID, layout->_layoutLen, ovlLen); for (uint32 oo=0; oogkStore_getNumReads() < iidMin) { - fprintf(stderr, "ERROR: only "F_U32" reads in the store (IDs 0-"F_U32" inclusive); can't process requested range -b "F_U32" -e "F_U32"\n", + fprintf(stderr, "ERROR: only " F_U32 " reads in the store (IDs 0-" F_U32 " inclusive); can't process requested range -b " F_U32 " -e " F_U32 "\n", gkpStore->gkStore_getNumReads(), gkpStore->gkStore_getNumReads()-1, iidMin, iidMax); diff --git a/src/erateEstimate/erateEstimate.C b/src/erateEstimate/erateEstimate.C index 9c0b447eb..26401fdde 100644 --- a/src/erateEstimate/erateEstimate.C +++ b/src/erateEstimate/erateEstimate.C @@ -297,7 +297,7 @@ recomputeErrorProfile(gkStore *gkpStore, uint64 nDiscard = 0; uint64 nRemain = 0; - fprintf(stderr, "Processing from IID "F_U32" to "F_U32" out of "F_U32" reads, iteration %u.\n", + fprintf(stderr, "Processing from IID " F_U32 " to " F_U32 " out of " F_U32 " reads, iteration %u.\n", iidMin, iidMin + numIIDs, gkpStore->gkStore_getNumReads(), @@ -394,9 +394,9 @@ recomputeErrorProfile(gkStore *gkpStore, // Report stats. fprintf(stderr, "\n"); - fprintf(stderr, "nDiscarded "F_U64" (in previous iterations)\n", nDiscarded); - fprintf(stderr, "nDiscard "F_U64" (in this iteration)\n", nDiscard); - fprintf(stderr, "nRemain "F_U64"\n", nRemain); + fprintf(stderr, "nDiscarded " F_U64 " (in previous iterations)\n", nDiscarded); + fprintf(stderr, "nDiscard " F_U64 " (in this iteration)\n", nDiscard); + fprintf(stderr, "nRemain " F_U64 "\n", nRemain); } @@ -425,7 +425,7 @@ outputOverlaps(gkStore *gkpStore, uint64 numOvls = inpStore->numOverlapsInRange(); - fprintf(stderr, "Processing from IID "F_U32" to "F_U32" out of "F_U32" reads.\n", + fprintf(stderr, "Processing from IID " F_U32 " to " F_U32 " out of " F_U32 " reads.\n", iidMin, iidMin + numIIDs, gkpStore->gkStore_getNumReads()); @@ -459,7 +459,7 @@ outputOverlaps(gkStore *gkpStore, } if ((no & 0x000fffff) == 0) - fprintf(stderr, " overlap %10"F_U64P" %8"F_U32P"-%8"F_U32P"\r", no, a_iid, b_iid); + fprintf(stderr, " overlap %10" F_U64P " %8" F_U32P "-%8" F_U32P "\r", no, a_iid, b_iid); } } @@ -497,8 +497,8 @@ outputOverlaps(gkStore *gkpStore, delete inpStore; fprintf(stderr, "\n"); - fprintf(stderr, "nDiscarded "F_U64" (in previous iterations)\n", nDiscarded); - fprintf(stderr, "nRemain "F_U64"\n", nRemain); + fprintf(stderr, "nDiscarded " F_U64 " (in previous iterations)\n", nDiscarded); + fprintf(stderr, "nRemain " F_U64 "\n", nRemain); } diff --git a/src/falcon_sense/createFalconSenseInputs.C b/src/falcon_sense/createFalconSenseInputs.C index 7bd36d553..46f7df4ef 100644 --- a/src/falcon_sense/createFalconSenseInputs.C +++ b/src/falcon_sense/createFalconSenseInputs.C @@ -138,7 +138,7 @@ main(int argc, char **argv) { if (numReadsPer > 0) numPartitions = nReadsInTigs / numReadsPer + 1; - fprintf(stderr, "Will partition "F_U64" total child reads into "F_U32" partitions.\n", + fprintf(stderr, "Will partition " F_U64 " total child reads into " F_U32 " partitions.\n", nReadsInTigs, numPartitions); // Decide on a partitioning, based on total reads per tig. diff --git a/src/falcon_sense/outputFalcon.C b/src/falcon_sense/outputFalcon.C index 97a10b4cc..8ed673138 100644 --- a/src/falcon_sense/outputFalcon.C +++ b/src/falcon_sense/outputFalcon.C @@ -54,7 +54,7 @@ outputFalcon(gkStore *gkpStore, gkpStore->gkStore_loadReadData(tig->tigID(), readData); - fprintf(F, "read"F_U32" %s\n", tig->tigID(), readData->gkReadData_getSequence()); + fprintf(F, "read" F_U32 " %s\n", tig->tigID(), readData->gkReadData_getSequence()); for (uint32 cc=0; ccnumberOfChildren(); cc++) { tgPosition *child = tig->getChild(cc); @@ -80,7 +80,7 @@ outputFalcon(gkStore *gkpStore, seq[ readData->gkReadData_getRead()->gkRead_sequenceLength() - child->_askip - child->_bskip ] = 0; } - fprintf(F, "data"F_U32" %s\n", tig->getChild(cc)->ident(), seq); + fprintf(F, "data" F_U32 " %s\n", tig->getChild(cc)->ident(), seq); } fprintf(F, "+ +\n"); diff --git a/src/fastq-utilities/fastqAnalyze.C b/src/fastq-utilities/fastqAnalyze.C index 94fecd6ba..37f3979cf 100644 --- a/src/fastq-utilities/fastqAnalyze.C +++ b/src/fastq-utilities/fastqAnalyze.C @@ -163,18 +163,18 @@ doStats(char *inName, totBases += ii; if ((totSeqs % 10000) == 0) - fprintf(stderr, "Reading "F_U64"\r", totSeqs); + fprintf(stderr, "Reading " F_U64 "\r", totSeqs); } - fprintf(stderr, "Read "F_U64"\n", totSeqs); + fprintf(stderr, "Read " F_U64 "\n", totSeqs); fprintf(stdout, "%s\n", inName); fprintf(stdout, "\n"); - fprintf(stdout, "sequences\t"F_U64"\n", totSeqs); - fprintf(stdout, "bases\t"F_U64"\n", totBases); + fprintf(stdout, "sequences\t" F_U64 "\n", totSeqs); + fprintf(stdout, "bases\t" F_U64 "\n", totBases); fprintf(stdout, "\n"); - fprintf(stdout, "average\t"F_U64"\n", totBases / totSeqs); + fprintf(stdout, "average\t" F_U64 "\n", totBases / totSeqs); fprintf(stdout, "\n"); //sort(seqLen.begin(), seqLen.end()); @@ -196,7 +196,7 @@ doStats(char *inName, histogram[seqLen[ii]]++; for (uint32 ii=min; ii<=max; ii++) - fprintf(stdout, F_U32"\t"F_U64"\n", ii, histogram[ii]); + fprintf(stdout, F_U32"\t" F_U64 "\n", ii, histogram[ii]); delete [] histogram; @@ -212,7 +212,7 @@ doStats(char *inName, freq->mono[ii] * 100.0 / totBases)); sort(output.begin(), output.end()); for (uint32 ii=0; iidi[ii][jj] * 100.0 / totBases)); sort(output.begin(), output.end()); for (uint32 ii=0; iitri[ii][jj][kk] * 100.0 / totBases)); sort(output.begin(), output.end()); for (uint32 ii=0; ii 0) { - sprintf(path1, "%s.x=%07.3f.n=%09"F_U64P".%c.fastq", OUTNAME, (double)nBasesToOutput / GENOMESIZE, nPairsToOutput, (isMated == true) ? '1' : 'u'); - sprintf(path2, "%s.x=%07.3f.n=%09"F_U64P".%c.fastq", OUTNAME, (double)nBasesToOutput / GENOMESIZE, nPairsToOutput, (isMated == true) ? '2' : 'u'); + sprintf(path1, "%s.x=%07.3f.n=%09" F_U64P ".%c.fastq", OUTNAME, (double)nBasesToOutput / GENOMESIZE, nPairsToOutput, (isMated == true) ? '1' : 'u'); + sprintf(path2, "%s.x=%07.3f.n=%09" F_U64P ".%c.fastq", OUTNAME, (double)nBasesToOutput / GENOMESIZE, nPairsToOutput, (isMated == true) ? '2' : 'u'); } else { - sprintf(path1, "%s.x=UNKNOWN.n=%09"F_U64P".%c.fastq", OUTNAME, nPairsToOutput, (isMated == true) ? '1' : 'u'); - sprintf(path2, "%s.x=UNKNOWN.n=%09"F_U64P".%c.fastq", OUTNAME, nPairsToOutput, (isMated == true) ? '2' : 'u'); + sprintf(path1, "%s.x=UNKNOWN.n=%09" F_U64P ".%c.fastq", OUTNAME, nPairsToOutput, (isMated == true) ? '1' : 'u'); + sprintf(path2, "%s.x=UNKNOWN.n=%09" F_U64P ".%c.fastq", OUTNAME, nPairsToOutput, (isMated == true) ? '2' : 'u'); } errno = 0; @@ -498,10 +498,10 @@ main(int argc, char **argv) { if (isMated == true) { if (nPairsToOutput > 0) - fprintf(stderr, "Extracting "F_U64" mate pairs into %s and %s\n", + fprintf(stderr, "Extracting " F_U64 " mate pairs into %s and %s\n", nPairsToOutput, path1, path2); else - fprintf(stderr, "Extracting "F_U64" bases of mate pairs into %s and %s\n", + fprintf(stderr, "Extracting " F_U64 " bases of mate pairs into %s and %s\n", nBasesToOutput, path1, path2); for (; Ar->read(Ai) && Br->read(Bi); i++) { @@ -521,10 +521,10 @@ main(int argc, char **argv) { } else { if (nPairsToOutput > 0) - fprintf(stderr, "Extracting "F_U64" reads into %s\n", + fprintf(stderr, "Extracting " F_U64 " reads into %s\n", nPairsToOutput, path1); else - fprintf(stderr, "Extracting "F_U64" bases of reads into %s\n", + fprintf(stderr, "Extracting " F_U64 " bases of reads into %s\n", nBasesToOutput, path1); for (; Ar->read(Ai); i++) { @@ -542,14 +542,14 @@ main(int argc, char **argv) { delete Br; if (i > totPairsInInput) { - fprintf(stderr, "WARNING: There are "F_U64" %s in the input; you claimed there are "F_U64" (-t option) %s.\n", + fprintf(stderr, "WARNING: There are " F_U64 " %s in the input; you claimed there are " F_U64 " (-t option) %s.\n", i, (isMated) ? "mates" : "reads", totPairsInInput, (isMated) ? "mates" : "reads"); fprintf(stderr, "WARNING: Result is not a random sample of the input file.\n"); } if (i < totPairsInInput) { - fprintf(stderr, "WARNING: There are "F_U64" %s in the input; you claimed there are "F_U64" (-t option) %s.\n", + fprintf(stderr, "WARNING: There are " F_U64 " %s in the input; you claimed there are " F_U64 " (-t option) %s.\n", i, (isMated) ? "mates" : "reads", totPairsInInput, (isMated) ? "mates" : "reads"); fprintf(stderr, "WARNING: Result is only %f X coverage.\n", (double)s * READLENGTH / GENOMESIZE); diff --git a/src/fastq-utilities/fastqSimulate-sort.C b/src/fastq-utilities/fastqSimulate-sort.C index 13af42a51..a4dbc170e 100644 --- a/src/fastq-utilities/fastqSimulate-sort.C +++ b/src/fastq-utilities/fastqSimulate-sort.C @@ -128,7 +128,7 @@ readRead(FILE *inFile, uint32 &seq, uint32 &bgn, uint32 &end) { end = strtoul(a+p, NULL, 10); - //fprintf(stderr, "seq="F_U32" bgn="F_U32" end="F_U32" line %s", + //fprintf(stderr, "seq=" F_U32 " bgn=" F_U32 " end=" F_U32 " line %s", // seq, bgn, end, a); char *retstr = new char [al + bl + cl + dl + 1]; @@ -249,7 +249,7 @@ main(int argc, char **argv) { reads.push_back(pr); } - fprintf(stderr, "Loaded "F_U64" mated reads.\n", reads.size()); + fprintf(stderr, "Loaded " F_U64 " mated reads.\n", reads.size()); sort(reads.begin(), reads.end()); diff --git a/src/fastq-utilities/fastqSimulate.C b/src/fastq-utilities/fastqSimulate.C index e5382a9c3..246e06080 100644 --- a/src/fastq-utilities/fastqSimulate.C +++ b/src/fastq-utilities/fastqSimulate.C @@ -997,7 +997,7 @@ main(int argc, char **argv) { // when the end of genome is hit. This is caught later in makeSequence() and the // read is aborted. - fprintf(stderr, "seed = "F_U64"\n", seed); + fprintf(stderr, "seed = " F_U64 "\n", seed); srand48(seed); memset(revComp, '&', sizeof(char) * 256); @@ -1204,10 +1204,10 @@ main(int argc, char **argv) { fprintf(stderr, "\n"); fprintf(stderr, "Number of reads with:\n"); - fprintf(stderr, " nNoChange = "F_U64"\n", nNoChange); - fprintf(stderr, " nMismatch = "F_U64"\n", nMismatch); - fprintf(stderr, " nInsert = "F_U64"\n", nInsert); - fprintf(stderr, " nDelete = "F_U64"\n", nDelete); + fprintf(stderr, " nNoChange = " F_U64 "\n", nNoChange); + fprintf(stderr, " nMismatch = " F_U64 "\n", nMismatch); + fprintf(stderr, " nInsert = " F_U64 "\n", nInsert); + fprintf(stderr, " nDelete = " F_U64 "\n", nDelete); exit(0); } diff --git a/src/merTrim/merTrim.C b/src/merTrim/merTrim.C index 6cc5b47ca..1b8b92fea 100644 --- a/src/merTrim/merTrim.C +++ b/src/merTrim/merTrim.C @@ -180,10 +180,10 @@ public: gktCur = gktBgn; if (gktBgn > gktEnd) - fprintf(stderr, "ERROR: invalid range: -b ("F_U32") >= -e ("F_U32").\n", + fprintf(stderr, "ERROR: invalid range: -b (" F_U32 ") >= -e (" F_U32 ").\n", gktBgn, gktEnd), exit(1); if (gktEnd > gkRead->gkStore_getNumFragments()) - fprintf(stderr, "ERROR: invalid range: -e ("F_U32") > num frags ("F_U32").\n", + fprintf(stderr, "ERROR: invalid range: -e (" F_U32 ") > num frags (" F_U32 ").\n", gktEnd, gkRead->gkStore_getNumFragments()), exit(1); errno = 0; @@ -223,28 +223,28 @@ public: uint32 i = 0; uint32 iX = 0; - //fprintf(stderr, "distinct: "F_U64"\n", MF->numberOfDistinctMers()); - //fprintf(stderr, "unique: "F_U64"\n", MF->numberOfUniqueMers()); - //fprintf(stderr, "total: "F_U64"\n", MF->numberOfTotalMers()); + //fprintf(stderr, "distinct: " F_U64 "\n", MF->numberOfDistinctMers()); + //fprintf(stderr, "unique: " F_U64 "\n", MF->numberOfUniqueMers()); + //fprintf(stderr, "total: " F_U64 "\n", MF->numberOfTotalMers()); - //fprintf(stderr, "Xcoverage zero 1 0 "F_U64"\n", MF->histogram(1)); + //fprintf(stderr, "Xcoverage zero 1 0 " F_U64 "\n", MF->histogram(1)); for (i=2; (i < MF->histogramLength()) && (MF->histogram(i-1) > MF->histogram(i)); i++) - //fprintf(stderr, "Xcoverage drop "F_U32" "F_U64" "F_U64"\n", i, MF->histogram(i-1), MF->histogram(i)); + //fprintf(stderr, "Xcoverage drop " F_U32 " " F_U64 " " F_U64 "\n", i, MF->histogram(i-1), MF->histogram(i)); ; iX = i - 1; for (; i < MF->histogramLength(); i++) { if (MF->histogram(iX) < MF->histogram(i)) { - //fprintf(stderr, "Xcoverage incr "F_U32" "F_U64" "F_U64"\n", i, MF->histogram(iX), MF->histogram(i)); + //fprintf(stderr, "Xcoverage incr " F_U32 " " F_U64 " " F_U64 "\n", i, MF->histogram(iX), MF->histogram(i)); iX = i; } else { - //fprintf(stderr, "Xcoverage drop "F_U32" "F_U64" "F_U64"\n", i, MF->histogram(iX), MF->histogram(i)); + //fprintf(stderr, "Xcoverage drop " F_U32 " " F_U64 " " F_U64 "\n", i, MF->histogram(iX), MF->histogram(i)); } } - fprintf(stderr, "Guessed X coverage is "F_U32"\n", iX); + fprintf(stderr, "Guessed X coverage is " F_U32 "\n", iX); delete MF; @@ -257,7 +257,7 @@ public: if (minVerifiedFraction > 0) minVerified = (uint32)floor(minVerifiedFraction * actualCoverage); - fprintf(stderr, "Use minCorrect="F_U32" minVerified="F_U32"\n", minCorrect, minVerified); + fprintf(stderr, "Use minCorrect=" F_U32 " minVerified=" F_U32 "\n", minCorrect, minVerified); if (minCorrect < minVerified) { fprintf(stderr, "WARNING!\n"); @@ -1229,7 +1229,7 @@ mertrimComputation::scoreAdapter(void) { containsAdapterEnd = MAX(containsAdapterEnd, end + 1); if (VERBOSE > 1) - log.add("ADAPTER at "F_U32","F_U32" ["F_U32","F_U32"]\n", + log.add("ADAPTER at " F_U32 "," F_U32 " [" F_U32 "," F_U32 "]\n", bgn, end, containsAdapterBgn, containsAdapterEnd); for (uint32 a=bgn; a<=end; a++) @@ -2155,7 +2155,7 @@ mertrimWriterFASTQ(mertrimGlobalData *g, mertrimComputation *s) { if (s->verifySeq) { } - fprintf(g->fqLog->file(), F_U32"\t"F_U32"\tchimer\t%c\t"F_U32"\t"F_U32"\tadapter\t%c\t"F_U32"\t"F_U32"\t"F_U32"\t"F_U32"\t%s\t%s\n", + fprintf(g->fqLog->file(), F_U32"\t" F_U32 "\tchimer\t%c\t" F_U32 "\t" F_U32 "\tadapter\t%c\t" F_U32 "\t" F_U32 "\t" F_U32 "\t" F_U32 "\t%s\t%s\n", s->clrBgn, s->clrEnd, s->suspectedChimer ? 't' : 'f', diff --git a/src/merTrim/merTrimResult.H b/src/merTrim/merTrimResult.H index c72d1a235..651be0d11 100644 --- a/src/merTrim/merTrimResult.H +++ b/src/merTrim/merTrimResult.H @@ -60,11 +60,11 @@ public: if (F == NULL) return; if (chimer) - fprintf(F, F_IID"\t"F_U32"\t"F_U32"\tchimer\t"F_U32"\t"F_U32"%s\n", + fprintf(F, F_IID"\t" F_U32 "\t" F_U32 "\tchimer\t" F_U32 "\t" F_U32 "%s\n", readIID, clrBgn, clrEnd, chmBgn, chmEnd, (deleted) ? "\tdeleted" : ""); else - fprintf(F, F_IID"\t"F_U32"\t"F_U32"%s\n", + fprintf(F, F_IID"\t" F_U32 "\t" F_U32 "%s\n", readIID, clrBgn, clrEnd, (deleted) ? "\tdeleted" : ""); }; diff --git a/src/mercy/mercy-regions.C b/src/mercy/mercy-regions.C index 9ef17a84c..50d06992a 100644 --- a/src/mercy/mercy-regions.C +++ b/src/mercy/mercy-regions.C @@ -78,7 +78,7 @@ readDepth(char *depthname, map*> &lowCoverage) { uint32 end = strtoul(W[3], 0L, 10); if (beg > end) - fprintf(stderr, "ERROR: l="F_U32" h="F_U32"\n", beg, end); + fprintf(stderr, "ERROR: l=" F_U32 " h=" F_U32 "\n", beg, end); if (ILs[uid] == 0L) ILs[uid] = new intervalList; @@ -90,7 +90,7 @@ readDepth(char *depthname, map*> &lowCoverage) { } fclose(F); - fprintf(stderr, " "F_U32" lines.\n", i); + fprintf(stderr, " " F_U32 " lines.\n", i); map*>::iterator it = ILs.begin(); map*>::iterator ed = ILs.end(); @@ -135,7 +135,7 @@ readVariation(char *depthname, map*> &variation) { } fclose(F); - fprintf(stderr, " "F_U32" lines.\n", i); + fprintf(stderr, " " F_U32 " lines.\n", i); } @@ -175,7 +175,7 @@ readBadMers(char *depthname, map*> &badMers) { } fclose(F); - fprintf(stderr, " "F_U32" lines.\n", i); + fprintf(stderr, " " F_U32 " lines.\n", i); } @@ -275,7 +275,7 @@ main(int argc, char **argv) { // We want to count the number of times a badmer region // begins/ends in some depth. - //fprintf(stderr, "testing beg "F_U32" "F_U32" -- "F_U32" "F_U32"\n", + //fprintf(stderr, "testing beg " F_U32 " " F_U32 " -- " F_U32 " " F_U32 "\n", // Ii->lo(ii), Ii->hi(ii), Id->lo(id), Id->hi(id)); uint32 beg = 0; @@ -285,7 +285,7 @@ main(int argc, char **argv) { while ((id < Id->numberOfIntervals()) && (Id->hi(id) <= Ii->lo(ii))) { id++; - //fprintf(stderr, "testing beg (m) "F_U32" "F_U32" -- "F_U32" "F_U32"\n", + //fprintf(stderr, "testing beg (m) " F_U32 " " F_U32 " -- " F_U32 " " F_U32 "\n", // Ii->lo(ii), Ii->hi(ii), Id->lo(id), Id->hi(id)); } if (id < Id->numberOfIntervals()) { @@ -296,23 +296,23 @@ main(int argc, char **argv) { if ((lo <= Ii->lo(ii)) && (Ii->lo(ii) < hi)) { beg = Id->depth(id); } else { - fprintf(stderr, "failed to find begin "F_U32" "F_U32" -- "F_U32" "F_U32" "F_U32"\n", + fprintf(stderr, "failed to find begin " F_U32 " " F_U32 " -- " F_U32 " " F_U32 " " F_U32 "\n", Ii->lo(ii), Ii->hi(ii), Id->lo(id), Id->hi(id), Id->depth(id)); if (id > 0) - fprintf(stderr, " "F_U32" "F_U32" -- "F_U32" "F_U32" "F_U32"\n", + fprintf(stderr, " " F_U32 " " F_U32 " -- " F_U32 " " F_U32 " " F_U32 "\n", Ii->lo(ii), Ii->hi(ii), Id->lo(id-1), Id->hi(id-1), Id->depth(id-1)); //exit(1); } } - //fprintf(stderr, "testing end "F_U64" "F_U64" -- "F_U64" "F_U64"\n", + //fprintf(stderr, "testing end " F_U64 " " F_U64 " -- " F_U64 " " F_U64 "\n", // Ii->lo(ii), Ii->hi(ii), Id->lo(id), Id->hi(id)); // High points can be equal. while ((id < Id->numberOfIntervals()) && (Id->hi(id) < Ii->hi(ii))) { id++; - //fprintf(stderr, "testing end (m) "F_U64" "F_U64" -- "F_U64" "F_U64"\n", + //fprintf(stderr, "testing end (m) " F_U64 " " F_U64 " -- " F_U64 " " F_U64 "\n", // Ii->lo(ii), Ii->hi(ii), Id->lo(id), Id->hi(id)); } if (id < Id->numberOfIntervals()) { @@ -323,10 +323,10 @@ main(int argc, char **argv) { if ((lo < Ii->hi(ii)) && (Ii->hi(ii) <= hi)) { end = Id->depth(id); } else { - fprintf(stderr, "failed to find end "F_U32" "F_U32" -- "F_U32" "F_U32" "F_U32"\n", + fprintf(stderr, "failed to find end " F_U32 " " F_U32 " -- " F_U32 " " F_U32 " " F_U32 "\n", Ii->lo(ii), Ii->hi(ii), Id->lo(id), Id->hi(id), Id->depth(id)); if (id > 0) - fprintf(stderr, " "F_U32" "F_U32" -- "F_U32" "F_U32" "F_U32"\n", + fprintf(stderr, " " F_U32 " " F_U32 " -- " F_U32 " " F_U32 " " F_U32 "\n", Ii->lo(ii), Ii->hi(ii), Id->lo(id-1), Id->hi(id-1), Id->depth(id-1)); //exit(1); } @@ -335,7 +335,7 @@ main(int argc, char **argv) { badBegDepth[beg]++; badEndDepth[end]++; - fprintf(stdout, F_U64"\t"F_U32"\t"F_U32"\tdepth="F_U32","F_U32"\n", + fprintf(stdout, F_U64"\t" F_U32 "\t" F_U32 "\tdepth=" F_U32 "," F_U32 "\n", uid, Ii->lo(ii), Ii->hi(ii), beg, end); if ((beg < 32) && (end < 32)) @@ -351,11 +351,11 @@ main(int argc, char **argv) { uint32 bb = 0; uint32 be = 0; for (uint32 x=0; x<32; x++) { - fprintf(stdout, F_U32"\t"F_U32"\t"F_U32"\n", x, badBegDepth[x], badEndDepth[x]); + fprintf(stdout, F_U32"\t" F_U32 "\t" F_U32 "\n", x, badBegDepth[x], badEndDepth[x]); bb += badBegDepth[x]; be += badEndDepth[x]; } - fprintf(stdout, "total\t"F_U32"\t"F_U32"\n", bb, be); + fprintf(stdout, "total\t" F_U32 "\t" F_U32 "\n", bb, be); for (uint32 i=0; i<30; i++) { for (uint32 j=0; j<30; j++) diff --git a/src/mercy/mercy.C b/src/mercy/mercy.C index 7fab726b8..956316828 100644 --- a/src/mercy/mercy.C +++ b/src/mercy/mercy.C @@ -86,7 +86,7 @@ findMode(char *name) { if (H[i] > H[mi]) mi = i; - fprintf(stderr, "Mode of '%s' is "F_U32"\n", name, mi); + fprintf(stderr, "Mode of '%s' is " F_U32 "\n", name, mi); return(mi); } @@ -149,9 +149,9 @@ compare(merylStreamReader *F, if (dumpFlag) if (Ftype == 0) if (Ctype == 1) - fprintf(dumpSCZF, ">"F_U32"\n%s\n", Ccnt, Cmer.merToString(merstring)); + fprintf(dumpSCZF, ">" F_U32 "\n%s\n", Ccnt, Cmer.merToString(merstring)); else - fprintf(dumpMCZF, ">"F_U32"\n%s\n", Ccnt, Cmer.merToString(merstring)); + fprintf(dumpMCZF, ">" F_U32 "\n%s\n", Ccnt, Cmer.merToString(merstring)); } return; } @@ -168,9 +168,9 @@ compare(merylStreamReader *F, // Again, save the mer since it's in contigs, but not fragments. if (dumpFlag) if (Ctype == 1) - fprintf(dumpSCZF, ">"F_U32"\n%s\n", Ccnt, Cmer.merToString(merstring)); + fprintf(dumpSCZF, ">" F_U32 "\n%s\n", Ccnt, Cmer.merToString(merstring)); else - fprintf(dumpMCZF, ">"F_U32"\n%s\n", Ccnt, Cmer.merToString(merstring)); + fprintf(dumpMCZF, ">" F_U32 "\n%s\n", Ccnt, Cmer.merToString(merstring)); } return; @@ -187,12 +187,12 @@ compare(merylStreamReader *F, if (dumpFlag) { if (Ftype < Ctype) if (Ctype == 2) - fprintf(dumpMCSF, ">"F_U32"\n%s\n", Ccnt, Cmer.merToString(merstring)); + fprintf(dumpMCSF, ">" F_U32 "\n%s\n", Ccnt, Cmer.merToString(merstring)); else - fprintf(dumpMCMF, ">"F_U32"\n%s\n", Ccnt, Cmer.merToString(merstring)); + fprintf(dumpMCMF, ">" F_U32 "\n%s\n", Ccnt, Cmer.merToString(merstring)); if ((Ftype == 0) && (Ctype == 1)) - fprintf(dumpSCZF, ">"F_U32"\n%s\n", Ccnt, Cmer.merToString(merstring)); + fprintf(dumpSCZF, ">" F_U32 "\n%s\n", Ccnt, Cmer.merToString(merstring)); } } @@ -216,7 +216,7 @@ output(char *title, default: fprintf(stdout, "????????? "); break; } for (uint32 j=0; j<5; j++) - fprintf(stdout, "%12"F_U32P, R[i][j]); + fprintf(stdout, "%12" F_U32P, R[i][j]); fprintf(stdout, "\n"); } } @@ -319,11 +319,11 @@ main(int argc, char **argv) { if (differ) { fprintf(stderr, "error: mer size differ.\n"); - fprintf(stderr, " AF - "F_U32"\n", ms[0]); - fprintf(stderr, " TF - "F_U32"\n", ms[1]); - fprintf(stderr, " AC - "F_U32"\n", ms[2]); - fprintf(stderr, " DC - "F_U32"\n", ms[3]); - fprintf(stderr, " CO - "F_U32"\n", ms[4]); + fprintf(stderr, " AF - " F_U32 "\n", ms[0]); + fprintf(stderr, " TF - " F_U32 "\n", ms[1]); + fprintf(stderr, " AC - " F_U32 "\n", ms[2]); + fprintf(stderr, " DC - " F_U32 "\n", ms[3]); + fprintf(stderr, " CO - " F_U32 "\n", ms[4]); exit(1); } diff --git a/src/meryl/estimate-mer-threshold.C b/src/meryl/estimate-mer-threshold.C index f788b25b7..e2b696fc8 100644 --- a/src/meryl/estimate-mer-threshold.C +++ b/src/meryl/estimate-mer-threshold.C @@ -78,9 +78,9 @@ main(int argc, char **argv) { uint64 total = 0; uint32 Xcoverage = 8; - fprintf(stderr, "distinct: "F_U64"\n", MF->numberOfDistinctMers()); - fprintf(stderr, "unique: "F_U64"\n", MF->numberOfUniqueMers()); - fprintf(stderr, "total: "F_U64"\n", MF->numberOfTotalMers()); + fprintf(stderr, "distinct: " F_U64 "\n", MF->numberOfDistinctMers()); + fprintf(stderr, "unique: " F_U64 "\n", MF->numberOfUniqueMers()); + fprintf(stderr, "total: " F_U64 "\n", MF->numberOfTotalMers()); // Pass 0: try to deduce the X coverage we have. The // pattern we should see in mer counts is an initial spike @@ -99,27 +99,27 @@ main(int argc, char **argv) { uint32 i = 0; uint32 iX = 0; - fprintf(stderr, "distinct: "F_U64"\n", MF->numberOfDistinctMers()); - fprintf(stderr, "unique: "F_U64"\n", MF->numberOfUniqueMers()); - fprintf(stderr, "total: "F_U64"\n", MF->numberOfTotalMers()); + fprintf(stderr, "distinct: " F_U64 "\n", MF->numberOfDistinctMers()); + fprintf(stderr, "unique: " F_U64 "\n", MF->numberOfUniqueMers()); + fprintf(stderr, "total: " F_U64 "\n", MF->numberOfTotalMers()); - fprintf(stderr, "Xcoverage zero 1 0 "F_U64"\n", MF->histogram(1)); + fprintf(stderr, "Xcoverage zero 1 0 " F_U64 "\n", MF->histogram(1)); for (i=2; (i < MF->histogramLength()) && (MF->histogram(i-1) > MF->histogram(i)); i++) - fprintf(stderr, "Xcoverage drop "F_U32" "F_U64" "F_U64"\n", i, MF->histogram(i-1), MF->histogram(i)); + fprintf(stderr, "Xcoverage drop " F_U32 " " F_U64 " " F_U64 "\n", i, MF->histogram(i-1), MF->histogram(i)); iX = i - 1; for (; i < MF->histogramLength(); i++) { if (MF->histogram(iX) < MF->histogram(i)) { - fprintf(stderr, "Xcoverage incr "F_U32" "F_U64" "F_U64"\n", i, MF->histogram(iX), MF->histogram(i)); + fprintf(stderr, "Xcoverage incr " F_U32 " " F_U64 " " F_U64 "\n", i, MF->histogram(iX), MF->histogram(i)); iX = i; } else { - //fprintf(stderr, "Xcoverage drop "F_U32" "F_U64" "F_U64"\n", i, MF->histogram(iX), MF->histogram(i)); + //fprintf(stderr, "Xcoverage drop " F_U32 " " F_U64 " " F_U64 "\n", i, MF->histogram(iX), MF->histogram(i)); } } - fprintf(stderr, "Guessed X coverage is "F_U32"\n", iX); + fprintf(stderr, "Guessed X coverage is " F_U32 "\n", iX); Xcoverage = iX; @@ -143,7 +143,7 @@ main(int argc, char **argv) { maxCount = i; } - fprintf(stderr, "Set maxCount to "F_U32", which will cover %.2f%% of distinct mers and %.2f%% of all mers.\n", + fprintf(stderr, "Set maxCount to " F_U32 ", which will cover %.2f%% of distinct mers and %.2f%% of all mers.\n", i, 100.0 * distinct / totalUsefulDistinct, 100.0 * total / totalUsefulAll); @@ -174,7 +174,7 @@ main(int argc, char **argv) { maxCount = i; - fprintf(stderr, "Reset maxCount to "F_U32", which will cover %.2f%% of distinct mers and %.2f%% of all mers.\n", + fprintf(stderr, "Reset maxCount to " F_U32 ", which will cover %.2f%% of distinct mers and %.2f%% of all mers.\n", maxCount, 100.0 * distinct / totalUsefulDistinct, 100.0 * total / totalUsefulAll); } diff --git a/src/meryl/leaff-blocks.C b/src/meryl/leaff-blocks.C index e0261f901..a1b14b3c1 100644 --- a/src/meryl/leaff-blocks.C +++ b/src/meryl/leaff-blocks.C @@ -62,7 +62,7 @@ seqCache *F = 0L; char seq = S->sequence()[pos]; if (nnn != V[seq]) { - fprintf(stdout, "%c "F_U32" "F_U32" "F_U32" "F_U32"\n", + fprintf(stdout, "%c " F_U32 " " F_U32 " " F_U32 " " F_U32 "\n", begseq, s, begpos, pos, pos - begpos); nnn = V[seq]; begpos = pos; @@ -70,9 +70,9 @@ seqCache *F = 0L; } } - fprintf(stdout, "%c "F_U32" "F_U32" "F_U32" "F_U32"\n", + fprintf(stdout, "%c " F_U32 " " F_U32 " " F_U32 " " F_U32 "\n", begseq, s, begpos, pos, pos - begpos); - fprintf(stdout, ". "F_U32" "F_U32" "F_U32"\n", s, pos, 0); + fprintf(stdout, ". " F_U32 " " F_U32 " " F_U32 "\n", s, pos, 0); delete S; } diff --git a/src/meryl/leaff-duplicates.C b/src/meryl/leaff-duplicates.C index 902d727ab..425b7522f 100644 --- a/src/meryl/leaff-duplicates.C +++ b/src/meryl/leaff-duplicates.C @@ -57,9 +57,9 @@ mapDuplicates_Print(char *filea, seqInCore *sa, char *fileb, seqInCore *sb) { if (strcmp(sa->sequence(), sb->sequence()) == 0) - fprintf(stdout, F_U32" <-> "F_U32"\n", sa->getIID(), sb->getIID()); + fprintf(stdout, F_U32" <-> " F_U32 "\n", sa->getIID(), sb->getIID()); else - fprintf(stderr, "COLLISION DETECTED BETWEEN %s:"F_U32" AND %s:"F_U32"!\nPLEASE REPORT THIS TO bri@walenz.org!\n", + fprintf(stderr, "COLLISION DETECTED BETWEEN %s:" F_U32 " AND %s:" F_U32 "!\nPLEASE REPORT THIS TO bri@walenz.org!\n", filea, sa->getIID(), fileb, sb->getIID()); } @@ -83,7 +83,7 @@ findDuplicates(char *filename) { for (uint32 idx=1; idxgetSequenceInCore(result[idx].i); if (strcmp(s1->sequence(), s2->sequence()) == 0) { - fprintf(stdout, F_U32":%s\n"F_U32":%s\n\n", + fprintf(stdout, F_U32":%s\n" F_U32 ":%s\n\n", result[idx-1].i, s1->header(), result[idx ].i, s2->header()); } else { - fprintf(stderr, "COLLISION DETECTED BETWEEN IID "F_U32" AND "F_U32"!\nPLEASE REPORT THIS TO bri@walenz.org!\n", + fprintf(stderr, "COLLISION DETECTED BETWEEN IID " F_U32 " AND " F_U32 "!\nPLEASE REPORT THIS TO bri@walenz.org!\n", result[idx-1].i, result[idx].i); } diff --git a/src/meryl/leaff-gc.C b/src/meryl/leaff-gc.C index 5daed023f..e179e07d7 100644 --- a/src/meryl/leaff-gc.C +++ b/src/meryl/leaff-gc.C @@ -98,7 +98,7 @@ computeGCcontent(char *filename) { ave1001 += g[i+500] - ((i > 500) ? g[i-501] : 0); ave2001 += g[i+1000] - ((i > 1000) ? g[i-1001] : 0); - fprintf(stdout, F_U32"\t"F_U32"\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", + fprintf(stdout, F_U32"\t" F_U32 "\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", i, s[i], ave3 / (double)((i >= 1) ? 3 - ((i < genomeLength - 1) ? 0 : i + 2 - genomeLength) : i+2), diff --git a/src/meryl/leaff-partition.C b/src/meryl/leaff-partition.C index f3387367f..2b521c00e 100644 --- a/src/meryl/leaff-partition.C +++ b/src/meryl/leaff-partition.C @@ -85,14 +85,14 @@ outputPartition(seqCache *F, // for (uint32 i=0; isequenceLength() != p[i].length) { - fprintf(stderr, "Huh? '%s' "F_U32" != "F_U32"\n", S->header(), S->sequenceLength(), p[i].length); + fprintf(stderr, "Huh? '%s' " F_U32 " != " F_U32 "\n", S->header(), S->sequenceLength(), p[i].length); } delete S; @@ -126,10 +126,10 @@ outputPartition(seqCache *F, for (uint32 i=0; igetSourceName()); fprintf(stdout, "\n"); - fprintf(stdout, "numSeqs "F_U32"\n", numSeq); + fprintf(stdout, "numSeqs " F_U32 "\n", numSeq); fprintf(stdout, "\n"); - fprintf(stdout, "SPAN (smallest "F_U32" largest "F_U32")\n", Ls[numSeq-1], Ls[0]); + fprintf(stdout, "SPAN (smallest " F_U32 " largest " F_U32 ")\n", Ls[numSeq-1], Ls[0]); for (uint32 i=1; i<10; i++) - fprintf(stdout, "n"F_U32" %10"F_U32P" at index "F_U32"\n", 10 * i, n50s[i], l50s[i]); - fprintf(stdout, "totLen %10"F_U64P"\n", Ss); - fprintf(stdout, "refLen %10"F_U64P"\n", Rs); + fprintf(stdout, "n" F_U32 " %10" F_U32P " at index " F_U32 "\n", 10 * i, n50s[i], l50s[i]); + fprintf(stdout, "totLen %10" F_U64P "\n", Ss); + fprintf(stdout, "refLen %10" F_U64P "\n", Rs); fprintf(stdout, "\n"); - fprintf(stdout, "BASES (smallest "F_U32" largest "F_U32")\n", Lb[numSeq-1], Lb[0]); + fprintf(stdout, "BASES (smallest " F_U32 " largest " F_U32 ")\n", Lb[numSeq-1], Lb[0]); for (uint32 i=1; i<10; i++) - fprintf(stdout, "n"F_U32" %10"F_U32P" at index "F_U32"\n", 10 * i, n50b[i], l50b[i]); - fprintf(stdout, "totLen %10"F_U64P"\n", Sb); - fprintf(stdout, "refLen %10"F_U64P"\n", Rb); + fprintf(stdout, "n" F_U32 " %10" F_U32P " at index " F_U32 "\n", 10 * i, n50b[i], l50b[i]); + fprintf(stdout, "totLen %10" F_U64P "\n", Sb); + fprintf(stdout, "refLen %10" F_U64P "\n", Rb); delete [] Ls; delete [] Lb; diff --git a/src/meryl/leaff.C b/src/meryl/leaff.C index dc3a49b50..25b9cca0e 100644 --- a/src/meryl/leaff.C +++ b/src/meryl/leaff.C @@ -361,7 +361,7 @@ void printSequence(uint32 sid) { seqInCore *sic = fasta->getSequenceInCore(sid); if (sic == 0L) - fprintf(stderr, "WARNING: Didn't find sequence with iid '"F_U32"'\n", sid); + fprintf(stderr, "WARNING: Didn't find sequence with iid '" F_U32 "'\n", sid); else printSequence(sic); delete sic; @@ -450,7 +450,7 @@ processArray(int argc, char **argv) { (argv[arg] == 0L) ? "(nullpointer)" : argv[arg]), exit(1); for (uint32 s=0; sgetNumberOfSequences(); s++) - fprintf(stdout, "G\tseq\t%s:"F_U32"\t"F_U32"\t%s\n", + fprintf(stdout, "G\tseq\t%s:" F_U32 "\t" F_U32 "\t%s\n", argv[arg], s, fasta->getSequenceLength(s), ">unimplemented"); } else if (strcmp(argv[arg], "-d") == 0) { @@ -519,7 +519,7 @@ processArray(int argc, char **argv) { seq[p++] = bases[MT.mtRandom32() & 0x3]; seq[p] = 0; - sprintf(def, "random%06"F_U32P, i); + sprintf(def, "random%06" F_U32P, i); printSequence(def, seq, 0, j); } @@ -787,7 +787,7 @@ processFile(char *filename) { errno = 0; len = fread(data+pos, 1, max - pos, F); if (errno) - fprintf(stderr, "Couldn't read "F_U64" bytes from '%s': %s\n", + fprintf(stderr, "Couldn't read " F_U64 " bytes from '%s': %s\n", (uint64)(max-pos), filename, strerror(errno)), exit(1); pos += len; diff --git a/src/meryl/libleaff/fastaFile.C b/src/meryl/libleaff/fastaFile.C index fdfc19615..fbca4b49b 100644 --- a/src/meryl/libleaff/fastaFile.C +++ b/src/meryl/libleaff/fastaFile.C @@ -141,7 +141,7 @@ uint32 fastaFile::getSequenceLength(uint32 iid) { #ifdef DEBUG - fprintf(stderr, "fastaFile::getSequenceLength()-- "F_U32"\n", iid); + fprintf(stderr, "fastaFile::getSequenceLength()-- " F_U32 "\n", iid); #endif return((iid < _numberOfSequences) ? _index[iid]._seqLength : 0); @@ -155,7 +155,7 @@ fastaFile::getSequence(uint32 iid, char *&s, uint32 &sLen, uint32 &sMax) { #ifdef DEBUG - fprintf(stderr, "fastaFile::getSequence(full)-- "F_U32"\n", iid); + fprintf(stderr, "fastaFile::getSequence(full)-- " F_U32 "\n", iid); #endif // Assume there is no index. Without being horribly complicated @@ -169,7 +169,7 @@ fastaFile::getSequence(uint32 iid, // use the seqFile instead. if (iid >= _header._numberOfSequences) { - fprintf(stderr, "fastaFile::getSequence(full)-- iid "F_U32" more than number of sequences "F_U32"\n", + fprintf(stderr, "fastaFile::getSequence(full)-- iid " F_U32 " more than number of sequences " F_U32 "\n", iid, _header._numberOfSequences); return(false); } @@ -194,7 +194,7 @@ fastaFile::getSequence(uint32 iid, sLen = 0; #ifdef DEBUG - fprintf(stderr, "fastaFile::getSequence(full)-- seek to iid="F_U32" at pos="F_U32"\n", + fprintf(stderr, "fastaFile::getSequence(full)-- seek to iid=" F_U32 " at pos=" F_U32 "\n", iid, _index[iid]._seqPosition); #endif _rb->seek(_index[iid]._seqPosition); @@ -270,13 +270,13 @@ fastaFile::getSequence(uint32 iid, uint32 bgn, uint32 end, char *s) { if (iid >= _header._numberOfSequences) { - fprintf(stderr, "fastaFile::getSequence(part)-- iid "F_U32" more than number of sequences "F_U32"\n", + fprintf(stderr, "fastaFile::getSequence(part)-- iid " F_U32 " more than number of sequences " F_U32 "\n", iid, _header._numberOfSequences); return(false); } #ifdef DEBUG - fprintf(stderr, "fastaFile::getSequence(part)-- "F_U32"\n", iid); + fprintf(stderr, "fastaFile::getSequence(part)-- " F_U32 "\n", iid); #endif // It is impossible to be efficient here; see the big comment in @@ -566,7 +566,7 @@ fastaFile::constructIndex(void) { _index[indexLen]._seqLength = seqLen; #ifdef DEBUG - fprintf(stderr, "INDEX iid="F_U32" len="F_U32" pos="F_U64"\n", + fprintf(stderr, "INDEX iid=" F_U32 " len=" F_U32 " pos=" F_U64 "\n", indexLen, seqLen, seqStart); #endif diff --git a/src/meryl/libleaff/fastaStdin.C b/src/meryl/libleaff/fastaStdin.C index 94055b322..57052eabb 100644 --- a/src/meryl/libleaff/fastaStdin.C +++ b/src/meryl/libleaff/fastaStdin.C @@ -137,7 +137,7 @@ fastaStdin::getSequence(uint32 iid, bool ret = true; #ifdef DEBUG - fprintf(stderr, "fastaStdin::getSequence(full)-- "F_U32"\n", iid); + fprintf(stderr, "fastaStdin::getSequence(full)-- " F_U32 "\n", iid); #endif if (iid == _nextIID) diff --git a/src/meryl/libleaff/fastqFile.C b/src/meryl/libleaff/fastqFile.C index f4c65f343..219fe48af 100644 --- a/src/meryl/libleaff/fastqFile.C +++ b/src/meryl/libleaff/fastqFile.C @@ -141,7 +141,7 @@ uint32 fastqFile::getSequenceLength(uint32 iid) { #ifdef DEBUG - fprintf(stderr, "fastqFile::getSequenceLength()-- "F_U32"\n", iid); + fprintf(stderr, "fastqFile::getSequenceLength()-- " F_U32 "\n", iid); #endif return((iid < _numberOfSequences) ? _index[iid]._seqLength : 0); @@ -155,11 +155,11 @@ fastqFile::getSequence(uint32 iid, char *&s, uint32 &sLen, uint32 &sMax) { #ifdef DEBUG - fprintf(stderr, "fastqFile::getSequence(full)-- "F_U32"\n", iid); + fprintf(stderr, "fastqFile::getSequence(full)-- " F_U32 "\n", iid); #endif if (iid >= _header._numberOfSequences) { - fprintf(stderr, "fastqFile::getSequence(full)-- iid "F_U32" more than number of sequences "F_U32"\n", + fprintf(stderr, "fastqFile::getSequence(full)-- iid " F_U32 " more than number of sequences " F_U32 "\n", iid, _header._numberOfSequences); return(false); } @@ -184,7 +184,7 @@ fastqFile::getSequence(uint32 iid, sLen = 0; #ifdef DEBUG - fprintf(stderr, "fastqFile::getSequence(full)-- seek to iid="F_U32" at pos="F_U32"\n", + fprintf(stderr, "fastqFile::getSequence(full)-- seek to iid=" F_U32 " at pos=" F_U32 "\n", iid, _index[iid]._seqPosition); #endif _rb->seek(_index[iid]._seqPosition); @@ -271,13 +271,13 @@ fastqFile::getSequence(uint32 iid, uint32 bgn, uint32 end, char *s) { if (iid >= _header._numberOfSequences) { - fprintf(stderr, "fastqFile::getSequence(part)-- iid "F_U32" more than number of sequences "F_U32"\n", + fprintf(stderr, "fastqFile::getSequence(part)-- iid " F_U32 " more than number of sequences " F_U32 "\n", iid, _header._numberOfSequences); return(false); } #ifdef DEBUG - fprintf(stderr, "fastqFile::getSequence(part)-- "F_U32"\n", iid); + fprintf(stderr, "fastqFile::getSequence(part)-- " F_U32 "\n", iid); #endif // Unlike the fasta version of this, we know that all the sequence is on one line. However, we @@ -550,7 +550,7 @@ fastqFile::constructIndex(void) { // Save to the index. if (indexLen >= indexMax) { - fprintf(stderr, "REALLOC len="F_U32" from "F_U32" to "F_U32"\n", indexLen, indexMax, indexMax * 2); + fprintf(stderr, "REALLOC len=" F_U32 " from " F_U32 " to " F_U32 "\n", indexLen, indexMax, indexMax * 2); indexMax *= 2; fastqFileIndex *et = new fastqFileIndex[indexMax]; memcpy(et, _index, sizeof(fastqFileIndex) * indexLen); @@ -564,7 +564,7 @@ fastqFile::constructIndex(void) { #if 0 if ((indexLen * sizeof(fastqFileIndex) > 131000) && (indexLen * sizeof(fastqFileIndex) < 131200)) - fprintf(stderr, "INDEX pos="F_U64" iid="F_U32" len="F_U32" pos="F_U64"\n", + fprintf(stderr, "INDEX pos=" F_U64 " iid=" F_U32 " len=" F_U32 " pos=" F_U64 "\n", indexLen * sizeof(fastqFileIndex), indexLen, seqLen, seqStart); #endif diff --git a/src/meryl/libleaff/fastqStdin.C b/src/meryl/libleaff/fastqStdin.C index d0e5f49f4..bb282fe73 100644 --- a/src/meryl/libleaff/fastqStdin.C +++ b/src/meryl/libleaff/fastqStdin.C @@ -141,7 +141,7 @@ fastqStdin::getSequence(uint32 iid, bool ret = true; #ifdef DEBUG - fprintf(stderr, "fastqStdin::getSequence(full)-- "F_U32"\n", iid); + fprintf(stderr, "fastqStdin::getSequence(full)-- " F_U32 "\n", iid); #endif if (iid == _nextIID) @@ -181,7 +181,7 @@ bool fastqStdin::getSequence(uint32 iid, uint32 bgn, uint32 end, char *s) { - fprintf(stderr, "fastqStdin::getSequence(part)-- ERROR! Used for random access on iid "F_U32" from position "F_U32"-"F_U32".\n", iid, bgn, end); + fprintf(stderr, "fastqStdin::getSequence(part)-- ERROR! Used for random access on iid " F_U32 " from position " F_U32 "-" F_U32 ".\n", iid, bgn, end); assert(0); return(false); } diff --git a/src/meryl/libleaff/seqCache.C b/src/meryl/libleaff/seqCache.C index 184e09b7e..f9ae881af 100644 --- a/src/meryl/libleaff/seqCache.C +++ b/src/meryl/libleaff/seqCache.C @@ -77,7 +77,7 @@ seqCache::getSequenceIID(char *name) { iid = _fb->find(name); #ifdef DEBUG - fprintf(stderr, "seqCache::getSequenceIID()-- '%s' -> "F_U32"\n", name, iid); + fprintf(stderr, "seqCache::getSequenceIID()-- '%s' -> " F_U32 "\n", name, iid); #endif return(iid); @@ -190,7 +190,7 @@ seqCache::loadAllSequences(void) { char *h=0L, *s=0L; if (_fb->getSequence(iid, h, hLen, hMax, s, sLen, sMax) == false) - fprintf(stderr, "seqCache::loadAllSequences()-- Failed to load iid "F_U32".\n", + fprintf(stderr, "seqCache::loadAllSequences()-- Failed to load iid " F_U32 ".\n", iid), exit(1); _cache[iid] = new seqInCore(iid, h, hLen, s, sLen, true); diff --git a/src/meryl/libleaff/seqStore.C b/src/meryl/libleaff/seqStore.C index cff9aa8e8..fb16afacf 100644 --- a/src/meryl/libleaff/seqStore.C +++ b/src/meryl/libleaff/seqStore.C @@ -155,7 +155,7 @@ seqStore::getSequence(uint32 iid, loadIndex(); if (iid >= _header._numberOfSequences) { - fprintf(stderr, "seqStore::getSequence(full)-- iid "F_U32" more than number of sequences "F_U32"\n", + fprintf(stderr, "seqStore::getSequence(full)-- iid " F_U32 " more than number of sequences " F_U32 "\n", iid, _header._numberOfSequences); return(false); } @@ -223,13 +223,13 @@ seqStore::getSequence(uint32 iid, loadIndex(); if (iid >= _header._numberOfSequences) { - fprintf(stderr, "seqStore::getSequence(part)-- iid "F_U32" more than number of sequences "F_U32"\n", + fprintf(stderr, "seqStore::getSequence(part)-- iid " F_U32 " more than number of sequences " F_U32 "\n", iid, _header._numberOfSequences); return(false); } if (bgn >= end) { - fprintf(stderr, "seqStore::getSequence(part)-- for iid "F_U32"; invalid bgn="F_U32" end="F_U32"; seqLen="F_U32"\n", + fprintf(stderr, "seqStore::getSequence(part)-- for iid " F_U32 "; invalid bgn=" F_U32 " end=" F_U32 "; seqLen=" F_U32 "\n", iid, bgn, end, _index[iid]._seqLength); return(false); } @@ -346,9 +346,9 @@ seqStore::loadIndex(void) { fread(&_header, sizeof(seqStoreHeader), 1, F); - //fprintf(stderr, "seqStore::seqStore()-- Allocating space for "F_U32" sequences ("F_U64"MB)\n", _header._numberOfSequences, _header._numberOfSequences * sizeof(seqStoreIndex) / 1024 / 1024); - //fprintf(stderr, "seqStore::seqStore()-- Allocating space for "F_U32" blocks ("F_U64"MB)\n", _header._numberOfBlocks, _header._numberOfBlocks * sizeof(seqStoreBlock) / 1024 / 1024); - //fprintf(stderr, "seqStore::seqStore()-- Allocating space for "F_U32" labels ("F_U64"MB)\n", _header._namesLength, _header._namesLength * sizeof(char) / 1024 / 1024); + //fprintf(stderr, "seqStore::seqStore()-- Allocating space for " F_U32 " sequences (" F_U64 "MB)\n", _header._numberOfSequences, _header._numberOfSequences * sizeof(seqStoreIndex) / 1024 / 1024); + //fprintf(stderr, "seqStore::seqStore()-- Allocating space for " F_U32 " blocks (" F_U64 "MB)\n", _header._numberOfBlocks, _header._numberOfBlocks * sizeof(seqStoreBlock) / 1024 / 1024); + //fprintf(stderr, "seqStore::seqStore()-- Allocating space for " F_U32 " labels (" F_U64 "MB)\n", _header._namesLength, _header._namesLength * sizeof(char) / 1024 / 1024); _index = new seqStoreIndex [_header._numberOfSequences]; _block = new seqStoreBlock [_header._numberOfBlocks]; @@ -436,7 +436,7 @@ constructSeqStore(char *filename, seqCache *inputseq) { filename, inputseq->getSourceName(), inputseq->getFileTypeName()); seqStoreHeader HEAD; - memset(&HEAD, sizeof(seqStoreHeader), 0); + memset(&HEAD, 0, sizeof(seqStoreHeader)); bitPackedFile *DATA = new bitPackedFile(filename, sizeof(seqStoreHeader), true); @@ -490,13 +490,13 @@ constructSeqStore(char *filename, seqCache *inputseq) { #if SEQSTOREBLOCK_MAXPOS < uint64MASK(32) if (sic->sequenceLength() > SEQSTOREBLOCK_MAXPOS) - fprintf(stderr, "constructSeqStore()-- sequence %s too long, must be shorter than "F_U64" Gbp.\n", + fprintf(stderr, "constructSeqStore()-- sequence %s too long, must be shorter than " F_U64 " Gbp.\n", sic->header(), SEQSTOREBLOCK_MAXPOS / 1024 / 1024 / 1024), exit(1); #endif #if SEQSTOREBLOCK_MAXIID < uint64MASK(32) if (sic->getIID() > SEQSTOREBLOCK_MAXPOS) - fprintf(stderr, "constructSeqStore()-- too many sequences, must be fewer than "F_U64".\n", + fprintf(stderr, "constructSeqStore()-- too many sequences, must be fewer than " F_U64 ".\n", SEQSTOREBLOCK_MAXIID), exit(1); #endif @@ -650,6 +650,6 @@ constructSeqStore(char *filename, seqCache *inputseq) { // ESTmapper depends on this output. - fprintf(stderr, "constructSeqStore()-- seqStore '%s' constructed ("F_U32" sequences, "F_U64" ACGT letters, "F_U32" ACGT blocks, "F_U32" GAP blocks).\n", + fprintf(stderr, "constructSeqStore()-- seqStore '%s' constructed (" F_U32 " sequences, " F_U64 " ACGT letters, " F_U32 " ACGT blocks, " F_U32 " GAP blocks).\n", filename, HEAD._numberOfSequences, HEAD._numberOfACGT, HEAD._numberOfBlocksACGT, HEAD._numberOfBlocksGAP); } diff --git a/src/meryl/libleaff/seqStream.C b/src/meryl/libleaff/seqStream.C index ec386899a..9adcf9285 100644 --- a/src/meryl/libleaff/seqStream.C +++ b/src/meryl/libleaff/seqStream.C @@ -44,7 +44,7 @@ seqStream::seqStream(const char *filename) { _idxLen = _file->getNumberOfSequences(); _idx = new seqStreamIndex [_idxLen + 1]; - //fprintf(stderr, "seqStream::seqStream()-- Allocating "F_U64"MB for seqStreamIndex on "F_U64" sequences.\n", + //fprintf(stderr, "seqStream::seqStream()-- Allocating " F_U64 "MB for seqStreamIndex on " F_U64 " sequences.\n", // _idxLen * sizeof(seqStreamIndex) / 1024 / 1024, _idxLen); _seqNumOfPos = 0L; @@ -169,7 +169,7 @@ seqStream::tradeSpaceForTime(void) { uint32 i = 0; uint32 s = 0; - //fprintf(stderr, "Allocating "F_U32" uint32s for seqNumOfPos.\n", _lengthOfSequences); + //fprintf(stderr, "Allocating " F_U32 " uint32s for seqNumOfPos.\n", _lengthOfSequences); _seqNumOfPos = new uint32 [_lengthOfSequences]; @@ -232,12 +232,12 @@ seqStream::rewind(void){ _streamPos = _bgn; _bufferPos = _bgn; - //fprintf(stderr, "seqStream::rewind()-- 1 currentIdx="F_U32" currentPos="F_U32" streamPos="F_U32" bufferPos="F_U32"\n", + //fprintf(stderr, "seqStream::rewind()-- 1 currentIdx=" F_U32 " currentPos=" F_U32 " streamPos=" F_U32 " bufferPos=" F_U32 "\n", // _currentIdx, _currentPos, _streamPos, _bufferPos); fillBuffer(); - //fprintf(stderr, "seqStream::rewind()-- 2 currentIdx="F_U32" currentPos="F_U32" streamPos="F_U32" bufferPos="F_U32"\n", + //fprintf(stderr, "seqStream::rewind()-- 2 currentIdx=" F_U32 " currentPos=" F_U32 " streamPos=" F_U32 " bufferPos=" F_U32 "\n", // _currentIdx, _currentPos, _streamPos, _bufferPos); } @@ -258,7 +258,7 @@ seqStream::setRange(uint64 bgn, uint64 end) { end = l; if ((bgn > l) || (end > l)) - fprintf(stderr, "seqStream::setRange()-- ERROR: range ("F_U64","F_U64") too big; only "F_U64" positions.\n", + fprintf(stderr, "seqStream::setRange()-- ERROR: range (" F_U64 "," F_U64 ") too big; only " F_U64 " positions.\n", bgn, end, l), exit(1); _bgn = bgn; @@ -290,7 +290,7 @@ seqStream::sequenceNumberOfPosition(uint64 p) { // sequence that p is in. if (_lengthOfSequences <= p) { - fprintf(stderr, "seqStream::sequenceNumberOfPosition()-- WARNING: position p="F_U64" too big; only "F_U64" positions.\n", + fprintf(stderr, "seqStream::sequenceNumberOfPosition()-- WARNING: position p=" F_U64 " too big; only " F_U64 " positions.\n", p, _lengthOfSequences); return(s); } @@ -354,7 +354,7 @@ seqStream::fillBuffer(void) { if (_currentPos < _idx[_currentIdx]._len) { #ifdef DEBUG - fprintf(stderr, "seqStream::fillBuffer()-- More Seq currentPos="F_U32" len="F_U32"\n", _currentPos, _idx[_currentIdx]._len); + fprintf(stderr, "seqStream::fillBuffer()-- More Seq currentPos=" F_U32 " len=" F_U32 "\n", _currentPos, _idx[_currentIdx]._len); #endif _bufferLen = MIN(_idx[_currentIdx]._len - _currentPos, _bufferMax); @@ -362,7 +362,7 @@ seqStream::fillBuffer(void) { _currentPos, _currentPos + _bufferLen, _buffer) == false) - fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #1 iid="F_U32" bgn="F_U32" end="F_U32"\n", + fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #1 iid=" F_U32 " bgn=" F_U32 " end=" F_U32 "\n", _idx[_currentIdx]._iid, _currentPos, _currentPos + _bufferLen), exit(1); return; @@ -377,7 +377,7 @@ seqStream::fillBuffer(void) { _currentIdx++; #ifdef DEBUG - fprintf(stderr, "seqStream::fillBuffer()-- New Seq currentPos="F_U32" len="F_U32"\n", _currentPos, _idx[_currentIdx]._len); + fprintf(stderr, "seqStream::fillBuffer()-- New Seq currentPos=" F_U32 " len=" F_U32 "\n", _currentPos, _idx[_currentIdx]._len); #endif // All done if there is no more sequence. @@ -408,7 +408,7 @@ seqStream::fillBuffer(void) { _currentPos, _currentPos + bl, _buffer + _bufferLen) == false) - fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #2 iid="F_U32" bgn="F_U32" end="F_U32"\n", + fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #2 iid=" F_U32 " bgn=" F_U32 " end=" F_U32 "\n", _idx[_currentIdx]._iid, _currentPos, _currentPos + bl), exit(1); _bufferLen += bl; diff --git a/src/meryl/libmeryl.C b/src/meryl/libmeryl.C index bd4d269c8..2bb93614c 100644 --- a/src/meryl/libmeryl.C +++ b/src/meryl/libmeryl.C @@ -208,20 +208,20 @@ merylStreamReader::merylStreamReader(const char *fn_, uint32 ms_) { _validMer = true; #ifdef SHOW_VARIABLES - fprintf(stderr, "_merSizeInBits = "F_U32"\n", _merSizeInBits); - fprintf(stderr, "_merCompression = "F_U32"\n", _merCompression); - fprintf(stderr, "_prefixSize = "F_U32"\n", _prefixSize); - fprintf(stderr, "_merDataSize = "F_U32"\n", _merDataSize); - fprintf(stderr, "_numUnique = "F_U64"\n", _numUnique); - fprintf(stderr, "_numDistinct = "F_U64"\n", _numDistinct); - fprintf(stderr, "_numTotal = "F_U64"\n", _numTotal); - fprintf(stderr, "_thisBucket = "F_U64"\n", _thisBucket); - fprintf(stderr, "_thisBucketSize = "F_U64"\n", _thisBucketSize); - fprintf(stderr, "_thisMerCount = "F_U64"\n", _thisMerCount); + fprintf(stderr, "_merSizeInBits = " F_U32 "\n", _merSizeInBits); + fprintf(stderr, "_merCompression = " F_U32 "\n", _merCompression); + fprintf(stderr, "_prefixSize = " F_U32 "\n", _prefixSize); + fprintf(stderr, "_merDataSize = " F_U32 "\n", _merDataSize); + fprintf(stderr, "_numUnique = " F_U64 "\n", _numUnique); + fprintf(stderr, "_numDistinct = " F_U64 "\n", _numDistinct); + fprintf(stderr, "_numTotal = " F_U64 "\n", _numTotal); + fprintf(stderr, "_thisBucket = " F_U64 "\n", _thisBucket); + fprintf(stderr, "_thisBucketSize = " F_U64 "\n", _thisBucketSize); + fprintf(stderr, "_thisMerCount = " F_U64 "\n", _thisMerCount); #endif if ((ms_ > 0) && (_merSizeInBits >> 1 != ms_)) { - fprintf(stderr, "merylStreamReader()-- ERROR: User requested mersize "F_U32" but '%s' is mersize "F_U32"\n", + fprintf(stderr, "merylStreamReader()-- ERROR: User requested mersize " F_U32 " but '%s' is mersize " F_U32 "\n", ms_, _filename, _merSizeInBits >> 1); exit(1); } diff --git a/src/meryl/meryl-args.C b/src/meryl/meryl-args.C index 897103b12..bf6aa4c39 100644 --- a/src/meryl/meryl-args.C +++ b/src/meryl/meryl-args.C @@ -58,7 +58,7 @@ writeString(const char *str, FILE *F) { } if (errno) { - fprintf(stderr, "writeString()-- Failed to write string of length "F_U32": %s\n", len, strerror(errno)); + fprintf(stderr, "writeString()-- Failed to write string of length " F_U32 ": %s\n", len, strerror(errno)); fprintf(stderr, "writeString()-- First 80 bytes of string is:\n"); fprintf(stderr, "%80.80s\n", str); return(false); diff --git a/src/meryl/meryl-binaryOp.C b/src/meryl/meryl-binaryOp.C index 31d628cde..54d9b5715 100644 --- a/src/meryl/meryl-binaryOp.C +++ b/src/meryl/meryl-binaryOp.C @@ -81,8 +81,8 @@ binaryOperations(merylArgs *args) { // if (A->merSize() != B->merSize()) { fprintf(stderr, "ERROR - mersizes are different!\n"); - fprintf(stderr, "ERROR - mersize of '%s' is "F_U32"\n", args->mergeFiles[0], A->merSize()); - fprintf(stderr, "ERROR - mersize of '%s' is "F_U32"\n", args->mergeFiles[1], B->merSize()); + fprintf(stderr, "ERROR - mersize of '%s' is " F_U32 "\n", args->mergeFiles[0], A->merSize()); + fprintf(stderr, "ERROR - mersize of '%s' is " F_U32 "\n", args->mergeFiles[1], B->merSize()); exit(1); } diff --git a/src/meryl/meryl-build.C b/src/meryl/meryl-build.C index 45e759a79..9fd4c014c 100644 --- a/src/meryl/meryl-build.C +++ b/src/meryl/meryl-build.C @@ -193,10 +193,10 @@ submitCountBatches(merylArgs *args) { fclose(F); if (args->sgeBuildOpt) - sprintf(cmd, "qsub -t 1-"F_U64" -cwd -b n -j y -o %s-count-\\$TASK_ID.err %s -N mc%s %s-count.sh", + sprintf(cmd, "qsub -t 1-" F_U64 " -cwd -b n -j y -o %s-count-\\$TASK_ID.err %s -N mc%s %s-count.sh", args->segmentLimit, args->outputFile, args->sgeBuildOpt, args->sgeJobName, args->outputFile); else - sprintf(cmd, "qsub -t 1-"F_U64" -cwd -b n -j y -o %s-count-\\$TASK_ID.err -N mc%s %s-count.sh", + sprintf(cmd, "qsub -t 1-" F_U64 " -cwd -b n -j y -o %s-count-\\$TASK_ID.err -N mc%s %s-count.sh", args->segmentLimit, args->outputFile, args->sgeJobName, args->outputFile); fprintf(stderr, "%s\n", cmd); if (system(cmd)) @@ -335,28 +335,28 @@ prepareBatch(merylArgs *args) { args->merDataWidth = args->merSize * 2 - args->numBuckets_log2; if (args->merDataWidth > SORTED_LIST_WIDTH * 64) { - fprintf(stderr, " numMersActual = "F_U64"\n", args->numMersActual); - fprintf(stderr, " mersPerBatch = "F_U64"\n", args->mersPerBatch); - fprintf(stderr, " basesPerBatch = "F_U64"\n", args->basesPerBatch); - fprintf(stderr, " numBuckets = "F_U64" ("F_U32" bits)\n", args->numBuckets, args->numBuckets_log2); - fprintf(stderr, " bucketPointerWidth = "F_U32"\n", args->bucketPointerWidth); - fprintf(stderr, " merDataWidth = "F_U32"\n", args->merDataWidth); + fprintf(stderr, " numMersActual = " F_U64 "\n", args->numMersActual); + fprintf(stderr, " mersPerBatch = " F_U64 "\n", args->mersPerBatch); + fprintf(stderr, " basesPerBatch = " F_U64 "\n", args->basesPerBatch); + fprintf(stderr, " numBuckets = " F_U64 " (" F_U32 " bits)\n", args->numBuckets, args->numBuckets_log2); + fprintf(stderr, " bucketPointerWidth = " F_U32 "\n", args->bucketPointerWidth); + fprintf(stderr, " merDataWidth = " F_U32 "\n", args->merDataWidth); fprintf(stderr, "Sorry! merSize too big! Increase KMER_WORDS in libbio.kmer.H\n"); exit(1); } if (args->beVerbose) { - fprintf(stderr, "Computing "F_U64" segments using "F_U32" threads and "F_U64"MB memory ("F_U64"MB if in one batch).\n", + fprintf(stderr, "Computing " F_U64 " segments using " F_U32 " threads and " F_U64 "MB memory (" F_U64 "MB if in one batch).\n", args->segmentLimit, args->numThreads, estimateMemory(args->merSize, args->mersPerBatch, args->positionsEnabled) * args->numThreads, estimateMemory(args->merSize, args->numMersActual, args->positionsEnabled)); - fprintf(stderr, " numMersActual = "F_U64"\n", args->numMersActual); - fprintf(stderr, " mersPerBatch = "F_U64"\n", args->mersPerBatch); - fprintf(stderr, " basesPerBatch = "F_U64"\n", args->basesPerBatch); - fprintf(stderr, " numBuckets = "F_U64" ("F_U32" bits)\n", args->numBuckets, args->numBuckets_log2); - fprintf(stderr, " bucketPointerWidth = "F_U32"\n", args->bucketPointerWidth); - fprintf(stderr, " merDataWidth = "F_U32"\n", args->merDataWidth); + fprintf(stderr, " numMersActual = " F_U64 "\n", args->numMersActual); + fprintf(stderr, " mersPerBatch = " F_U64 "\n", args->mersPerBatch); + fprintf(stderr, " basesPerBatch = " F_U64 "\n", args->basesPerBatch); + fprintf(stderr, " numBuckets = " F_U64 " (" F_U32 " bits)\n", args->numBuckets, args->numBuckets_log2); + fprintf(stderr, " bucketPointerWidth = " F_U32 "\n", args->bucketPointerWidth); + fprintf(stderr, " merDataWidth = " F_U32 "\n", args->merDataWidth); } } @@ -379,17 +379,17 @@ runSegment(merylArgs *args, uint64 segment) { // XXX: This should check that the files are complete meryl files. // char *filename = new char [strlen(args->outputFile) + 17]; - sprintf(filename, "%s.batch"F_U64".mcdat", args->outputFile, segment); + sprintf(filename, "%s.batch" F_U64 ".mcdat", args->outputFile, segment); if (AS_UTL_fileExists(filename)) { if (args->beVerbose) - fprintf(stderr, "Found result for batch "F_U64" in %s.\n", segment, filename); + fprintf(stderr, "Found result for batch " F_U64 " in %s.\n", segment, filename); delete [] filename; return; } if ((args->beVerbose) && (args->segmentLimit > 1)) - fprintf(stderr, "Computing segment "F_U64" of "F_U64".\n", segment+1, args->segmentLimit); + fprintf(stderr, "Computing segment " F_U64 " of " F_U64 ".\n", segment+1, args->segmentLimit); delete [] filename; @@ -397,12 +397,12 @@ runSegment(merylArgs *args, uint64 segment) { // Allocate space for bucket pointers and (temporary) bucket sizes. if (args->beVerbose) - fprintf(stderr, " Allocating "F_U64"MB for bucket pointer table ("F_U32" bits wide).\n", + fprintf(stderr, " Allocating " F_U64 "MB for bucket pointer table (" F_U32 " bits wide).\n", (args->numBuckets * args->bucketPointerWidth + 128) >> 23, args->bucketPointerWidth); bucketPointers = new uint64 [(args->numBuckets * args->bucketPointerWidth + 128) >> 6]; if (args->beVerbose) - fprintf(stderr, " Allocating "F_U64"MB for counting the size of each bucket.\n", args->numBuckets >> 18); + fprintf(stderr, " Allocating " F_U64 "MB for counting the size of each bucket.\n", args->numBuckets >> 18); bucketSizes = new uint32 [ args->numBuckets ]; for (uint64 i=args->numBuckets; i--; ) bucketSizes[i] = uint32ZERO; @@ -483,7 +483,7 @@ runSegment(merylArgs *args, uint64 segment) { // All done with the counting table, get rid of it. if (args->beVerbose) - fprintf(stderr, " Releasing "F_U64"MB from counting the size of each bucket.\n", args->numBuckets >> 18); + fprintf(stderr, " Releasing " F_U64 "MB from counting the size of each bucket.\n", args->numBuckets >> 18); delete [] bucketSizes; @@ -492,7 +492,7 @@ runSegment(merylArgs *args, uint64 segment) { // allocate full words. if (args->beVerbose) - fprintf(stderr, " Allocating "F_U64"MB for mer storage ("F_U32" bits wide).\n", + fprintf(stderr, " Allocating " F_U64 "MB for mer storage (" F_U32 " bits wide).\n", (args->basesPerBatch * args->merDataWidth + 64) >> 23, args->merDataWidth); for (uint64 mword=0, width=args->merDataWidth; width > 0; ) { @@ -510,7 +510,7 @@ runSegment(merylArgs *args, uint64 segment) { if (args->positionsEnabled) { if (args->beVerbose) - fprintf(stderr, " Allocating "F_U64"MB for mer position storage.\n", + fprintf(stderr, " Allocating " F_U64 "MB for mer position storage.\n", (args->basesPerBatch * 32 + 32) >> 23); merPosnArray = new uint32 [ args->basesPerBatch + 1 ]; } @@ -568,7 +568,7 @@ runSegment(merylArgs *args, uint64 segment) { delete M; char *batchOutputFile = new char [strlen(args->outputFile) + 33]; - sprintf(batchOutputFile, "%s.batch"F_U64, args->outputFile, segment); + sprintf(batchOutputFile, "%s.batch" F_U64, args->outputFile, segment); C = new speedCounter(" Writing output: %7.2f Mmers -- %5.2f Mmers/second\r", 1000000.0, 0x1fffff, args->beVerbose); W = new merylStreamWriter((args->segmentLimit == 1) ? args->outputFile : batchOutputFile, @@ -588,20 +588,20 @@ runSegment(merylArgs *args, uint64 segment) { uint64 ed = getDecodedValue(bucketPointers, bucketPos, args->bucketPointerWidth); if (ed < st) { - fprintf(stderr, "ERROR: In segment "F_U64"\n", segment); - fprintf(stderr, "ERROR: Bucket "F_U64" (out of "F_U64") ends before it starts!\n", + fprintf(stderr, "ERROR: In segment " F_U64 "\n", segment); + fprintf(stderr, "ERROR: Bucket " F_U64 " (out of " F_U64 ") ends before it starts!\n", bucket, args->numBuckets); - fprintf(stderr, "ERROR: start="F_U64"\n", st); - fprintf(stderr, "ERROR: end ="F_U64"\n", ed); + fprintf(stderr, "ERROR: start=" F_U64 "\n", st); + fprintf(stderr, "ERROR: end =" F_U64 "\n", ed); } assert(ed >= st); if ((ed - st) > (uint64ONE << 30)) { - fprintf(stderr, "ERROR: In segment "F_U64"\n", segment); - fprintf(stderr, "ERROR: Bucket "F_U64" (out of "F_U64") is HUGE!\n", + fprintf(stderr, "ERROR: In segment " F_U64 "\n", segment); + fprintf(stderr, "ERROR: Bucket " F_U64 " (out of " F_U64 ") is HUGE!\n", bucket, args->numBuckets); - fprintf(stderr, "ERROR: start="F_U64"\n", st); - fprintf(stderr, "ERROR: end ="F_U64"\n", ed); + fprintf(stderr, "ERROR: start=" F_U64 "\n", st); + fprintf(stderr, "ERROR: end =" F_U64 "\n", ed); } // Nothing here? Keep going. @@ -703,7 +703,7 @@ runSegment(merylArgs *args, uint64 segment) { delete [] bucketPointers; if (args->beVerbose) - fprintf(stderr, "Segment "F_U64" finished.\n", segment); + fprintf(stderr, "Segment " F_U64 " finished.\n", segment); } @@ -740,7 +740,7 @@ build(merylArgs *args) { } else { fprintf(stdout, "Batch prepared. Please run:\n"); for (uint64 s=0; ssegmentLimit; s++) - fprintf(stdout, "%s -countbatch "F_U64" -o %s\n", args->execName, s, args->outputFile); + fprintf(stdout, "%s -countbatch " F_U64 " -o %s\n", args->execName, s, args->outputFile); fprintf(stdout, "%s -mergebatch -o %s\n", args->execName, args->outputFile); } } @@ -811,7 +811,7 @@ build(merylArgs *args) { argv[argc++] = "-s"; arga[argc] = true; argv[argc] = new char [strlen(args->outputFile) + 33]; - sprintf(argv[argc], "%s.batch"F_U32, args->outputFile, i); + sprintf(argv[argc], "%s.batch" F_U32, args->outputFile, i); argc++; } @@ -835,11 +835,11 @@ build(merylArgs *args) { char *filename = new char [strlen(args->outputFile) + 17]; for (uint32 i=0; isegmentLimit; i++) { - sprintf(filename, "%s.batch"F_U32".mcidx", args->outputFile, i); + sprintf(filename, "%s.batch" F_U32 ".mcidx", args->outputFile, i); unlink(filename); - sprintf(filename, "%s.batch"F_U32".mcdat", args->outputFile, i); + sprintf(filename, "%s.batch" F_U32 ".mcdat", args->outputFile, i); unlink(filename); - sprintf(filename, "%s.batch"F_U32".mcpos", args->outputFile, i); + sprintf(filename, "%s.batch" F_U32 ".mcpos", args->outputFile, i); unlink(filename); } diff --git a/src/meryl/meryl-dump.C b/src/meryl/meryl-dump.C index b4156e460..f6caed6bc 100644 --- a/src/meryl/meryl-dump.C +++ b/src/meryl/meryl-dump.C @@ -59,7 +59,7 @@ dumpThreshold(merylArgs *args) { while (M->nextMer()) { if (M->theCount() >= args->numMersEstimated) - fprintf(stdout, ">"F_U64"\n%s\n", + fprintf(stdout, ">" F_U64 "\n%s\n", M->theCount(), M->theFMer().merToString(str)); } @@ -77,9 +77,9 @@ dumpPositions(merylArgs *args) { fprintf(stderr, "File '%s' contains no position information.\n", args->inputFile); } else { while (M->nextMer()) { - fprintf(stdout, ">"F_U64, M->theCount()); + fprintf(stdout, ">" F_U64, M->theCount()); for (uint32 i=0; itheCount(); i++) - fprintf(stdout, " "F_U32, M->getPosition(i)); + fprintf(stdout, " " F_U32, M->getPosition(i)); fprintf(stdout, "\n%s\n", M->theFMer().merToString(str)); } } @@ -114,9 +114,9 @@ countUnique(merylArgs *args) { fprintf(stderr, "OK\n"); #endif - fprintf(stdout, "Found "F_U64" mers.\n", M->numberOfTotalMers()); - fprintf(stdout, "Found "F_U64" distinct mers.\n", M->numberOfDistinctMers()); - fprintf(stdout, "Found "F_U64" unique mers.\n", M->numberOfUniqueMers()); + fprintf(stdout, "Found " F_U64 " mers.\n", M->numberOfTotalMers()); + fprintf(stdout, "Found " F_U64 " distinct mers.\n", M->numberOfDistinctMers()); + fprintf(stdout, "Found " F_U64 " unique mers.\n", M->numberOfUniqueMers()); delete M; } @@ -129,11 +129,11 @@ plotHistogram(merylArgs *args) { merylStreamReader *M = new merylStreamReader(args->inputFile); - fprintf(stderr, "Found "F_U64" mers.\n", M->numberOfTotalMers()); - fprintf(stderr, "Found "F_U64" distinct mers.\n", M->numberOfDistinctMers()); - fprintf(stderr, "Found "F_U64" unique mers.\n", M->numberOfUniqueMers()); + fprintf(stderr, "Found " F_U64 " mers.\n", M->numberOfTotalMers()); + fprintf(stderr, "Found " F_U64 " distinct mers.\n", M->numberOfDistinctMers()); + fprintf(stderr, "Found " F_U64 " unique mers.\n", M->numberOfUniqueMers()); - fprintf(stderr, "Largest mercount is "F_U64".\n", + fprintf(stderr, "Largest mercount is " F_U64 ".\n", M->histogramMaximumCount()); for (uint32 i=1; ihistogramLength(); i++) { @@ -143,7 +143,7 @@ plotHistogram(merylArgs *args) { distinct += hist; total += hist * i; - fprintf(stdout, F_U32"\t"F_U64"\t%.4f\t%.4f\n", + fprintf(stdout, F_U32"\t" F_U64 "\t%.4f\t%.4f\n", i, hist, distinct / (double)M->numberOfDistinctMers(), @@ -192,10 +192,10 @@ dumpDistanceBetweenMers(merylArgs *args) { for (uint32 d=0; d> 3) * numThreads / 1048576.0, @@ -167,7 +167,7 @@ optimalNumberOfBuckets(uint32 merSize, for (h=2; h<=hmax && h<2*merSize; h++) { s = (uint64ONE << h) * hwidth + numMers * (2 * merSize - h + posPerMer); - //fprintf(stderr, "optimalNumberOfBuckets()-- h="F_U64" s="F_U64"\n", h, s); + //fprintf(stderr, "optimalNumberOfBuckets()-- h=" F_U64 " s=" F_U64 "\n", h, s); if (s < opts) { opth = h; @@ -205,6 +205,6 @@ estimate(merylArgs *args) { uint32 opth = optimalNumberOfBuckets(args->merSize, args->numMersEstimated, args->positionsEnabled); uint64 memu = ((uint64ONE << opth) * logBaseTwo64(args->numMersEstimated+1) + args->numMersEstimated * (2 * args->merSize - opth)); - fprintf(stderr, F_U64" "F_U32"-mers can be computed using "F_U64"MB memory.\n", + fprintf(stderr, F_U64" " F_U32 "-mers can be computed using " F_U64 "MB memory.\n", args->numMersEstimated, args->merSize, memu >> 23); } diff --git a/src/meryl/meryl-merge.C b/src/meryl/meryl-merge.C index a8e34308b..b6fa337fd 100644 --- a/src/meryl/meryl-merge.C +++ b/src/meryl/meryl-merge.C @@ -49,7 +49,7 @@ void multipleOperations(merylArgs *args) { if (args->mergeFilesLen < 2) { - fprintf(stderr, "ERROR - must have at least two databases (you gave "F_U32")!\n", args->mergeFilesLen); + fprintf(stderr, "ERROR - must have at least two databases (you gave " F_U32 ")!\n", args->mergeFilesLen); exit(1); } if (args->outputFile == 0L) { diff --git a/src/meryl/simple.C b/src/meryl/simple.C index 7a2b3b10b..f67de2e28 100644 --- a/src/meryl/simple.C +++ b/src/meryl/simple.C @@ -145,7 +145,7 @@ main(int argc, char **argv) { numMers = M->approximateNumberOfMers(); delete M; - fprintf(stderr, "Guessing "F_U64" mers in input '%s'\n", numMers, inName); + fprintf(stderr, "Guessing " F_U64 " mers in input '%s'\n", numMers, inName); M = new merStream(new kMerBuilder(merSize, merCompression), new seqStream(inName), @@ -160,7 +160,7 @@ main(int argc, char **argv) { uint64 theMersMax = 2 * numMers; // for allowing both -f and -r uint32 *theMers = new uint32 [theMersMax]; - fprintf(stderr, "Allocating "F_U64"MB for mer storage.\n", numMers * sizeof(uint64) >> 20); + fprintf(stderr, "Allocating " F_U64 "MB for mer storage.\n", numMers * sizeof(uint64) >> 20); C = new speedCounter(" Filling mer list: %7.2f Mmers -- %5.2f Mmers/second\r", 1000000.0, 0x1fffff, 1); @@ -180,7 +180,7 @@ main(int argc, char **argv) { delete C; delete M; - fprintf(stderr, "Found "F_U64" mers in input '%s'\n", theMersLen, inName); + fprintf(stderr, "Found " F_U64 " mers in input '%s'\n", theMersLen, inName); if (theMersLen > theMersMax) fprintf(stderr, "ERROR: too many mers in input!\n"), exit(1); @@ -212,7 +212,7 @@ main(int argc, char **argv) { uint64 numCounts = ((uint64)1) << (2 * merSize); uint32 *theCounts = new uint32 [numCounts]; - fprintf(stderr, "Allocating "F_U64"MB for count storage.\n", numCounts * sizeof(uint32) >> 20); + fprintf(stderr, "Allocating " F_U64 "MB for count storage.\n", numCounts * sizeof(uint32) >> 20); memset(theCounts, 0, sizeof(uint32) * numCounts); diff --git a/src/overlapBasedTrimming/splitReads-subReads.C b/src/overlapBasedTrimming/splitReads-subReads.C index 2994c85d2..8b2b3185b 100644 --- a/src/overlapBasedTrimming/splitReads-subReads.C +++ b/src/overlapBasedTrimming/splitReads-subReads.C @@ -287,7 +287,7 @@ detectSubReads(gkStore *gkp, numSpan += (doCheckSubRead(gkp, w->adj[ii].a_iid)) ? 1 : 2; if (subreadFile) - fprintf(subreadFile, "AcheckSub region %u ("F_S32"-"F_S32") with %u hits %u bighits - span %u largePalindrome %s\n", + fprintf(subreadFile, "AcheckSub region %u (" F_S32 "-" F_S32 ") with %u hits %u bighits - span %u largePalindrome %s\n", w->adj[0].a_iid, BAD.lo(bb), BAD.hi(bb), BAD.count(bb), allHits, numSpan, largePalindrome ? "true" : "false"); diff --git a/src/overlapBasedTrimming/splitReads.C b/src/overlapBasedTrimming/splitReads.C index a90e1a89b..cebebb5f0 100644 --- a/src/overlapBasedTrimming/splitReads.C +++ b/src/overlapBasedTrimming/splitReads.C @@ -222,7 +222,7 @@ main(int argc, char **argv) { if (idMax > gkp->gkStore_getNumReads()) idMax = gkp->gkStore_getNumReads(); - fprintf(stderr, "Processing from ID "F_U32" to "F_U32" out of "F_U32" reads, using errorRate = %.2f\n", + fprintf(stderr, "Processing from ID " F_U32 " to " F_U32 " out of " F_U32 " reads, using errorRate = %.2f\n", idMin, idMax, gkp->gkStore_getNumReads(), @@ -412,55 +412,55 @@ main(int argc, char **argv) { //fprintf(staFile, "%7u (use only overlaps longer than this)\n", minAlignLength); // NOT SUPPORTED! fprintf(staFile, "INPUT READS:\n"); fprintf(staFile, "-----------\n"); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (reads processed)\n", readsIn.nReads, readsIn.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (reads not processed, previously deleted)\n", deletedIn.nReads, deletedIn.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (reads not processed, in a library where trimming isn't allowed)\n", noTrimIn.nReads, noTrimIn.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (reads processed)\n", readsIn.nReads, readsIn.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (reads not processed, previously deleted)\n", deletedIn.nReads, deletedIn.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (reads not processed, in a library where trimming isn't allowed)\n", noTrimIn.nReads, noTrimIn.nBases); fprintf(staFile, "\n"); fprintf(staFile, "PROCESSED:\n"); fprintf(staFile, "--------\n"); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (no overlaps)\n", noOverlaps.nReads, noOverlaps.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (no coverage after adjusting for trimming done already)\n", noCoverage.nReads, noCoverage.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (processed for chimera)\n", readsProcChimera.nReads, readsProcChimera.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (processed for spur)\n", readsProcSpur.nReads, readsProcSpur.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (processed for subreads)\n", readsProcSubRead.nReads, readsProcSubRead.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (no overlaps)\n", noOverlaps.nReads, noOverlaps.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (no coverage after adjusting for trimming done already)\n", noCoverage.nReads, noCoverage.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (processed for chimera)\n", readsProcChimera.nReads, readsProcChimera.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (processed for spur)\n", readsProcSpur.nReads, readsProcSpur.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (processed for subreads)\n", readsProcSubRead.nReads, readsProcSubRead.nBases); fprintf(staFile, "\n"); fprintf(staFile, "READS WITH SIGNALS:\n"); fprintf(staFile, "------------------\n"); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" signals (number of 5' spur signal)\n", readsBadSpur5.nReads, readsBadSpur5.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" signals (number of 3' spur signal)\n", readsBadSpur3.nReads, readsBadSpur3.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" signals (number of chimera signal)\n", readsBadChimera.nReads, readsBadChimera.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" signals (number of subread signal)\n", readsBadSubread.nReads, readsBadSubread.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " signals (number of 5' spur signal)\n", readsBadSpur5.nReads, readsBadSpur5.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " signals (number of 3' spur signal)\n", readsBadSpur3.nReads, readsBadSpur3.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " signals (number of chimera signal)\n", readsBadChimera.nReads, readsBadChimera.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " signals (number of subread signal)\n", readsBadSubread.nReads, readsBadSubread.nBases); fprintf(staFile, "\n"); fprintf(staFile, "SIGNALS:\n"); fprintf(staFile, "-------\n"); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (size of 5' spur signal)\n", basesBadSpur5.nReads, basesBadSpur5.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (size of 3' spur signal)\n", basesBadSpur3.nReads, basesBadSpur3.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (size of chimera signal)\n", basesBadChimera.nReads, basesBadChimera.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (size of subread signal)\n", basesBadSubread.nReads, basesBadSubread.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (size of 5' spur signal)\n", basesBadSpur5.nReads, basesBadSpur5.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (size of 3' spur signal)\n", basesBadSpur3.nReads, basesBadSpur3.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (size of chimera signal)\n", basesBadChimera.nReads, basesBadChimera.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (size of subread signal)\n", basesBadSubread.nReads, basesBadSubread.nBases); fprintf(staFile, "\n"); fprintf(staFile, "TRIMMING:\n"); fprintf(staFile, "--------\n"); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (trimmed from the 5' end of the read)\n", readsTrimmed5.nReads, readsTrimmed5.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (trimmed from the 3' end of the read)\n", readsTrimmed3.nReads, readsTrimmed3.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (trimmed from the 5' end of the read)\n", readsTrimmed5.nReads, readsTrimmed5.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (trimmed from the 3' end of the read)\n", readsTrimmed3.nReads, readsTrimmed3.nBases); #if 0 fprintf(staFile, "DELETED:\n"); fprintf(staFile, "-------\n"); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (deleted because of both cimera and spur signals)\n", bothDeletedSmall.nReads, bothDeletedSmall.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (deleted because of chimera signal)\n", chimeraDeletedSmall.nReads, chimeraDeletedSmall.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (deleted because of spur signal)\n", spurDeletedSmall.nReads, spurDeletedSmall.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (deleted because of both cimera and spur signals)\n", bothDeletedSmall.nReads, bothDeletedSmall.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (deleted because of chimera signal)\n", chimeraDeletedSmall.nReads, chimeraDeletedSmall.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (deleted because of spur signal)\n", spurDeletedSmall.nReads, spurDeletedSmall.nBases); fprintf(staFile, "\n"); fprintf(staFile, "SPUR TYPES:\n"); fprintf(staFile, "----------\n"); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (normal spur detected)\n", spurDetectedNormal.nReads, spurDetectedNormal.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (linker spur detected)\n", spurDetectedLinker.nReads, spurDetectedLinker.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (normal spur detected)\n", spurDetectedNormal.nReads, spurDetectedNormal.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (linker spur detected)\n", spurDetectedLinker.nReads, spurDetectedLinker.nBases); fprintf(staFile, "\n"); fprintf(staFile, "CHIMERA TYPES:\n"); fprintf(staFile, "-------------\n"); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (innie-pair chimera detected)\n", chimeraDetectedInnie.nReads, chimeraDetectedInnie.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (overhanging chimera detected)\n", chimeraDetectedOverhang.nReads, chimeraDetectedOverhang.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (gap chimera detected)\n", chimeraDetectedGap.nReads, chimeraDetectedGap.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (linker chimera detected)\n", chimeraDetectedLinker.nReads, chimeraDetectedLinker.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (innie-pair chimera detected)\n", chimeraDetectedInnie.nReads, chimeraDetectedInnie.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (overhanging chimera detected)\n", chimeraDetectedOverhang.nReads, chimeraDetectedOverhang.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (gap chimera detected)\n", chimeraDetectedGap.nReads, chimeraDetectedGap.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (linker chimera detected)\n", chimeraDetectedLinker.nReads, chimeraDetectedLinker.nBases); #endif // INPUT READS = ACCEPTED + TRIMMED + DELETED diff --git a/src/overlapBasedTrimming/trimReads-largestCovered.C b/src/overlapBasedTrimming/trimReads-largestCovered.C index a21745513..18b9895a8 100644 --- a/src/overlapBasedTrimming/trimReads-largestCovered.C +++ b/src/overlapBasedTrimming/trimReads-largestCovered.C @@ -80,10 +80,10 @@ largestCovered(ovOverlap *ovl, #if 0 for (uint32 it=0; it 1) for (uint32 it=0; itgkRead_readID(), IL.lo(it), IL.hi(it)); + fprintf(stderr, "IL[%02d] - iid %d - " F_S64 " " F_S64 "\n", it, read->gkRead_readID(), IL.lo(it), IL.hi(it)); #endif if (IL.numberOfIntervals() == 0) { diff --git a/src/overlapBasedTrimming/trimReads-quality.C b/src/overlapBasedTrimming/trimReads-quality.C index 9877d83af..92eb4ef76 100644 --- a/src/overlapBasedTrimming/trimReads-quality.C +++ b/src/overlapBasedTrimming/trimReads-quality.C @@ -151,7 +151,7 @@ findGoodQuality(double *qltD, flen = fpos; rlen = rpos; - //fprintf(stderr, "qltLen = "F_U32" flen="F_U32" rlen="F_U32"\n", qltLen, flen, rlen); + //fprintf(stderr, "qltLen = " F_U32 " flen=" F_U32 " rlen=" F_U32 "\n", qltLen, flen, rlen); uint32 winningFPos = 0; uint32 winningRPos = 0; @@ -230,7 +230,7 @@ findGoodQuality(double *qltD, } else { - fprintf(stderr, "UNMATCHED OVERLAP\t"F_U32"\t"F_U32"\t"F_U32"\t"F_U32"\n", + fprintf(stderr, "UNMATCHED OVERLAP\t" F_U32 "\t" F_U32 "\t" F_U32 "\t" F_U32 "\n", f[fpos].start, f[fpos].end, r[rpos].start, r[rpos].end); } } diff --git a/src/overlapBasedTrimming/trimReads.C b/src/overlapBasedTrimming/trimReads.C index fa41500bf..2ab82eaa0 100644 --- a/src/overlapBasedTrimming/trimReads.C +++ b/src/overlapBasedTrimming/trimReads.C @@ -259,7 +259,7 @@ main(int argc, char **argv) { if (idMax > gkp->gkStore_getNumReads()) idMax = gkp->gkStore_getNumReads(); - fprintf(stderr, "Processing from ID "F_U32" to "F_U32" out of "F_U32" reads.\n", + fprintf(stderr, "Processing from ID " F_U32 " to " F_U32 " out of " F_U32 " reads.\n", idMin, idMax, gkp->gkStore_getNumReads()); @@ -379,7 +379,7 @@ main(int argc, char **argv) { outClr->setend(id) = fend; outClr->setDeleted(id); // Gah, just obliterates the clear range. - fprintf(logFile, F_U32"\t"F_U32"\t"F_U32"\t"F_U32"\t"F_U32"\tNOV%s\n", + fprintf(logFile, F_U32"\t" F_U32 "\t" F_U32 "\t" F_U32 "\t" F_U32 "\tNOV%s\n", id, ibgn, iend, fbgn, fend, @@ -393,7 +393,7 @@ main(int argc, char **argv) { outClr->setend(id) = fend; outClr->setDeleted(id); // Gah, just obliterates the clear range. - fprintf(logFile, F_U32"\t"F_U32"\t"F_U32"\t"F_U32"\t"F_U32"\tDEL%s\n", + fprintf(logFile, F_U32"\t" F_U32 "\t" F_U32 "\t" F_U32 "\t" F_U32 "\tDEL%s\n", id, ibgn, iend, fbgn, fend, @@ -406,7 +406,7 @@ main(int argc, char **argv) { (iend == fend)) { noChangeOut += read->gkRead_sequenceLength(); - fprintf(logFile, F_U32"\t"F_U32"\t"F_U32"\t"F_U32"\t"F_U32"\tNOC%s\n", + fprintf(logFile, F_U32"\t" F_U32 "\t" F_U32 "\t" F_U32 "\t" F_U32 "\tNOC%s\n", id, ibgn, iend, fbgn, fend, @@ -428,7 +428,7 @@ main(int argc, char **argv) { if (fbgn - ibgn > 0) trim5 += fbgn - ibgn; if (iend - fend > 0) trim3 += iend - fend; - fprintf(logFile, F_U32"\t"F_U32"\t"F_U32"\t"F_U32"\t"F_U32"\tMOD%s\n", + fprintf(logFile, F_U32"\t" F_U32 "\t" F_U32 "\t" F_U32 "\t" F_U32 "\tMOD%s\n", id, ibgn, iend, fbgn, fend, @@ -476,9 +476,9 @@ main(int argc, char **argv) { fprintf(staFile, "INPUT READS:\n"); fprintf(staFile, "-----------\n"); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (reads processed)\n", readsIn.nReads, readsIn.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (reads not processed, previously deleted)\n", deletedIn.nReads, deletedIn.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (reads not processed, in a library where trimming isn't allowed)\n", noTrimIn.nReads, noTrimIn.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (reads processed)\n", readsIn.nReads, readsIn.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (reads not processed, previously deleted)\n", deletedIn.nReads, deletedIn.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (reads not processed, in a library where trimming isn't allowed)\n", noTrimIn.nReads, noTrimIn.nBases); readsIn .generatePlots(outputPrefix, "inputReads", 250); deletedIn.generatePlots(outputPrefix, "inputDeletedReads", 250); @@ -487,10 +487,10 @@ main(int argc, char **argv) { fprintf(staFile, "\n"); fprintf(staFile, "OUTPUT READS:\n"); fprintf(staFile, "------------\n"); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (trimmed reads output)\n", readsOut.nReads, readsOut.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (reads with no change, kept as is)\n", noChangeOut.nReads, noChangeOut.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (reads with no overlaps, deleted)\n", noOvlOut.nReads, noOvlOut.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (reads with short trimmed length, deleted)\n", deletedOut.nReads, deletedOut.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (trimmed reads output)\n", readsOut.nReads, readsOut.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (reads with no change, kept as is)\n", noChangeOut.nReads, noChangeOut.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (reads with no overlaps, deleted)\n", noOvlOut.nReads, noOvlOut.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (reads with short trimmed length, deleted)\n", deletedOut.nReads, deletedOut.nBases); readsOut .generatePlots(outputPrefix, "outputTrimmedReads", 250); noOvlOut .generatePlots(outputPrefix, "outputNoOvlReads", 250); @@ -500,8 +500,8 @@ main(int argc, char **argv) { fprintf(staFile, "\n"); fprintf(staFile, "TRIMMING DETAILS:\n"); fprintf(staFile, "----------------\n"); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (bases trimmed from the 5' end of a read)\n", trim5.nReads, trim5.nBases); - fprintf(staFile, "%6"F_U32P" reads %12"F_U64P" bases (bases trimmed from the 3' end of a read)\n", trim3.nReads, trim3.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (bases trimmed from the 5' end of a read)\n", trim5.nReads, trim5.nBases); + fprintf(staFile, "%6" F_U32P " reads %12" F_U64P " bases (bases trimmed from the 3' end of a read)\n", trim3.nReads, trim3.nBases); trim5.generatePlots(outputPrefix, "trim5", 25); trim3.generatePlots(outputPrefix, "trim3", 25); diff --git a/src/overlapErrorAdjustment/analyzeAlignment.C b/src/overlapErrorAdjustment/analyzeAlignment.C index e8434b669..9d302d9a0 100644 --- a/src/overlapErrorAdjustment/analyzeAlignment.C +++ b/src/overlapErrorAdjustment/analyzeAlignment.C @@ -292,7 +292,7 @@ analyzeAlignment::analyze(char *aSeq, int32 aLen, int32 aOffset, void analyzeAlignment::outputDetails(uint32 j) { - fprintf(stderr, "%3"F_U32P": %c conf %3"F_U64P" deletes %3"F_U64P" | subst %3"F_U64P" %3"F_U64P" %3"F_U64P" %3"F_U64P" | no_insert %3"F_U64P" insert %3"F_U64P" %3"F_U64P" %3"F_U64P" %3"F_U64P"\n", + fprintf(stderr, "%3" F_U32P ": %c conf %3" F_U64P " deletes %3" F_U64P " | subst %3" F_U64P " %3" F_U64P " %3" F_U64P " %3" F_U64P " | no_insert %3" F_U64P " insert %3" F_U64P " %3" F_U64P " %3" F_U64P " %3" F_U64P "\n", j, _seq[j], _vote[j].confirmed, @@ -403,14 +403,14 @@ analyzeAlignment::generateCorrections(FILE *corFile) { // (total > 1) if (total <= 1) { - fprintf(stderr, "FEW total = "F_U64" <= 1\n", total); + fprintf(stderr, "FEW total = " F_U64 " <= 1\n", total); skippedTooFew++; continue; } // (2 * max > total) if (2 * max <= total) { - fprintf(stderr, "WEAK 2*max = "F_U64" <= total = "F_U64"\n", 2*max, total); + fprintf(stderr, "WEAK 2*max = " F_U64 " <= total = " F_U64 "\n", 2*max, total); skippedTooWeak++; continue; } @@ -424,7 +424,7 @@ analyzeAlignment::generateCorrections(FILE *corFile) { // ((haplo_ct < 2) || (Use_Haplo_Ct == false)) if ((haplo_ct >= 2) && (Use_Haplo_Ct == true)) { - fprintf(stderr, "HAPLO haplo_ct="F_U64" >= 2 AND Use_Haplo_Ct = %s\n", haplo_ct, (Use_Haplo_Ct) ? "true" : "false"); + fprintf(stderr, "HAPLO haplo_ct=" F_U64 " >= 2 AND Use_Haplo_Ct = %s\n", haplo_ct, (Use_Haplo_Ct) ? "true" : "false"); skippedHaplo++; continue; } @@ -433,7 +433,7 @@ analyzeAlignment::generateCorrections(FILE *corFile) { // ((_vote[j].confirmed == 1) && (max > 6))) if ((_vote[j].confirmed > 0) && ((_vote[j].confirmed != 1) || (max <= 6))) { - fprintf(stderr, "INDET confirmed = "F_U64" max = "F_U64"\n", _vote[j].confirmed, max); + fprintf(stderr, "INDET confirmed = " F_U64 " max = " F_U64 "\n", _vote[j].confirmed, max); skippedConfirmed++; continue; } @@ -442,7 +442,7 @@ analyzeAlignment::generateCorrections(FILE *corFile) { substitutions++; - fprintf(stderr, "SUBSTITUTE position "F_U32" to %c\n", j, Matching_Char(vval)); + fprintf(stderr, "SUBSTITUTE position " F_U32 " to %c\n", j, Matching_Char(vval)); _cor[_corLen].type = vval; _cor[_corLen].pos = j; @@ -485,26 +485,26 @@ analyzeAlignment::generateCorrections(FILE *corFile) { _vote[j].t_insert); if (ins_total <= 1) { - fprintf(stderr, "FEW ins_total = "F_U64" <= 1\n", ins_total); + fprintf(stderr, "FEW ins_total = " F_U64 " <= 1\n", ins_total); skippedInsTotal++; continue; } if (2 * ins_max >= ins_total) { - fprintf(stderr, "WEAK 2*ins_max = "F_U64" <= ins_total = "F_U64"\n", 2*ins_max, ins_total); + fprintf(stderr, "WEAK 2*ins_max = " F_U64 " <= ins_total = " F_U64 "\n", 2*ins_max, ins_total); skippedInsMax++; continue; } if ((ins_haplo_ct >= 2) && (Use_Haplo_Ct == true)) { - fprintf(stderr, "HAPLO ins_haplo_ct="F_U64" >= 2 AND Use_Haplo_Ct = %s\n", ins_haplo_ct, (Use_Haplo_Ct) ? "true" : "false"); + fprintf(stderr, "HAPLO ins_haplo_ct=" F_U64 " >= 2 AND Use_Haplo_Ct = %s\n", ins_haplo_ct, (Use_Haplo_Ct) ? "true" : "false"); skippedInsHaplo++; continue; } if ((_vote[j].no_insert > 0) && ((_vote[j].no_insert != 1) || (ins_max <= 6))) { - fprintf(stderr, "INDET no_insert = "F_U64" ins_max = "F_U64"\n", _vote[j].no_insert, ins_max); + fprintf(stderr, "INDET no_insert = " F_U64 " ins_max = " F_U64 "\n", _vote[j].no_insert, ins_max); skippedInsTooMany++; continue; } @@ -513,7 +513,7 @@ analyzeAlignment::generateCorrections(FILE *corFile) { insertions++; - fprintf(stderr, "INSERT position "F_U32" to %c\n", j, Matching_Char(ins_vote)); + fprintf(stderr, "INSERT position " F_U32 " to %c\n", j, Matching_Char(ins_vote)); _cor[_corLen].type = ins_vote; _cor[_corLen].pos = j; @@ -547,7 +547,7 @@ analyzeAlignment::generateCorrections(FILE *corFile) { #if 0 - fprintf(stderr, "Corrected "F_U64" bases with "F_U64" substitutions, "F_U64" deletions and "F_U64" insertions.\n", + fprintf(stderr, "Corrected " F_U64 " bases with " F_U64 " substitutions, " F_U64 " deletions and " F_U64 " insertions.\n", G->basesLen, changes[A_SUBST] + changes[C_SUBST] + changes[G_SUBST] + changes[T_SUBST], changes[DELETE], diff --git a/src/overlapErrorAdjustment/correctOverlaps-Correct_Frags.C b/src/overlapErrorAdjustment/correctOverlaps-Correct_Frags.C index d7166fb33..b8e0666c2 100644 --- a/src/overlapErrorAdjustment/correctOverlaps-Correct_Frags.C +++ b/src/overlapErrorAdjustment/correctOverlaps-Correct_Frags.C @@ -91,7 +91,7 @@ correctRead(uint32 curID, if ((i != C[Cpos].pos) && (i != C[Cpos].pos + 1)) - fprintf(stderr, "i="F_U32" Cpos="F_U64" C[Cpos].pos="F_U32"\n", i, Cpos, C[Cpos].pos); + fprintf(stderr, "i=" F_U32 " Cpos=" F_U64 " C[Cpos].pos=" F_U32 "\n", i, Cpos, C[Cpos].pos); assert((i == C[Cpos].pos) || (i == C[Cpos].pos + 1)); @@ -215,7 +215,7 @@ Correct_Frags(coParameters *G, uint64 firstRecord = 0; uint64 currentRecord = 0; - fprintf(stderr, "Reading "F_U64" corrections from '%s'.\n", Clen, G->correctionsName); + fprintf(stderr, "Reading " F_U64 " corrections from '%s'.\n", Clen, G->correctionsName); // Count the number of bases, so we can do two gigantic allocations for bases and adjustments. // Adjustments are always less than the number of corrections; we could also count exactly. @@ -241,9 +241,9 @@ Correct_Frags(coParameters *G, } } - fprintf(stderr, "Correcting "F_U64" bases with "F_U64" indel adjustments.\n", G->basesLen, G->adjustsLen); + fprintf(stderr, "Correcting " F_U64 " bases with " F_U64 " indel adjustments.\n", G->basesLen, G->adjustsLen); - fprintf(stderr, "--Allocate "F_U64" + "F_U64" + "F_U64" MB for bases, adjusts and reads.\n", + fprintf(stderr, "--Allocate " F_U64 " + " F_U64 " + " F_U64 " MB for bases, adjusts and reads.\n", (sizeof(char) * G->basesLen) >> 20, (sizeof(Adjust_t) * G->adjustsLen) >> 20, (sizeof(Frag_Info_t) * (G->endID - G->bgnID + 1)) >> 20); @@ -285,7 +285,7 @@ Correct_Frags(coParameters *G, // We should be at the IDENT message. if (C[Cpos].type != IDENT) { - fprintf(stderr, "ERROR: didn't find IDENT at Cpos="F_U64" for read "F_U32"\n", Cpos, curID); + fprintf(stderr, "ERROR: didn't find IDENT at Cpos=" F_U64 " for read " F_U32 "\n", Cpos, curID); fprintf(stderr, " C[Cpos] = keep_left=%u keep_right=%u type=%u pos=%u readID=%u\n", C[Cpos].keep_left, C[Cpos].keep_right, @@ -324,7 +324,7 @@ Correct_Frags(coParameters *G, delete readData; delete Cfile; - fprintf(stderr, "Corrected "F_U64" bases with "F_U64" substitutions, "F_U64" deletions and "F_U64" insertions.\n", + fprintf(stderr, "Corrected " F_U64 " bases with " F_U64 " substitutions, " F_U64 " deletions and " F_U64 " insertions.\n", G->basesLen, changes[A_SUBST] + changes[C_SUBST] + changes[G_SUBST] + changes[T_SUBST], changes[DELETE], diff --git a/src/overlapErrorAdjustment/correctOverlaps-Read_Olaps.C b/src/overlapErrorAdjustment/correctOverlaps-Read_Olaps.C index e845f7fc4..eb88a6cb3 100644 --- a/src/overlapErrorAdjustment/correctOverlaps-Read_Olaps.C +++ b/src/overlapErrorAdjustment/correctOverlaps-Read_Olaps.C @@ -44,10 +44,10 @@ Read_Olaps(coParameters *G, gkStore *gkpStore) { uint64 numNormal = 0; uint64 numInnie = 0; - fprintf(stderr, "Read_Olaps()-- Loading "F_U64" overlaps from '%s' for reads "F_U32" to "F_U32"\n", + fprintf(stderr, "Read_Olaps()-- Loading " F_U64 " overlaps from '%s' for reads " F_U32 " to " F_U32 "\n", numolaps, G->ovlStorePath, G->bgnID, G->endID); - fprintf(stderr, "--Allocate "F_U64" MB for overlaps.\n", + fprintf(stderr, "--Allocate " F_U64 " MB for overlaps.\n", (sizeof(Olap_Info_t) * numolaps) >> 20); G->olaps = new Olap_Info_t [numolaps]; @@ -75,7 +75,7 @@ Read_Olaps(coParameters *G, gkStore *gkpStore) { delete ovs; - fprintf(stderr, "Read_Olaps()-- Loaded "F_U64" overlaps -- "F_U64" normal and "F_U64" innie.\n", + fprintf(stderr, "Read_Olaps()-- Loaded " F_U64 " overlaps -- " F_U64 " normal and " F_U64 " innie.\n", G->olapsLen, numNormal, numInnie); } diff --git a/src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C b/src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C index 2cede2254..ada0c4e7a 100644 --- a/src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C +++ b/src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C @@ -290,19 +290,19 @@ Redo_Olaps(coParameters *G, gkStore *gkpStore) { // Allocate some temporary work space for the forward and reverse corrected B reads. - fprintf(stderr, "--Allocate "F_U64" MB for fseq and rseq.\n", (2 * sizeof(char) * 2 * (AS_MAX_READLEN + 1)) >> 20); + fprintf(stderr, "--Allocate " F_U64 " MB for fseq and rseq.\n", (2 * sizeof(char) * 2 * (AS_MAX_READLEN + 1)) >> 20); char *fseq = new char [AS_MAX_READLEN + 1 + AS_MAX_READLEN + 1]; uint32 fseqLen = 0; char *rseq = new char [AS_MAX_READLEN + 1 + AS_MAX_READLEN + 1]; uint32 rseqLen = 0; - fprintf(stderr, "--Allocate "F_U64" MB for fadj and radj.\n", (2 * sizeof(Adjust_t) * (AS_MAX_READLEN + 1)) >> 20); + fprintf(stderr, "--Allocate " F_U64 " MB for fadj and radj.\n", (2 * sizeof(Adjust_t) * (AS_MAX_READLEN + 1)) >> 20); Adjust_t *fadj = new Adjust_t [AS_MAX_READLEN + 1]; Adjust_t *radj = new Adjust_t [AS_MAX_READLEN + 1]; uint32 fadjLen = 0; // radj is the same length - fprintf(stderr, "--Allocate "F_U64" MB for pedWorkArea_t.\n", sizeof(pedWorkArea_t) >> 20); + fprintf(stderr, "--Allocate " F_U64 " MB for pedWorkArea_t.\n", sizeof(pedWorkArea_t) >> 20); gkReadData *readData = new gkReadData; pedWorkArea_t *ped = new pedWorkArea_t; @@ -540,14 +540,14 @@ Redo_Olaps(coParameters *G, gkStore *gkpStore) { delete [] G->adjusts; G->adjusts = NULL; delete [] G->reads; G->reads = NULL; - fprintf(stderr, "Olaps Fwd "F_U64"\n", olapsFwd); - fprintf(stderr, "Olaps Rev "F_U64"\n", olapsRev); + fprintf(stderr, "Olaps Fwd " F_U64 "\n", olapsFwd); + fprintf(stderr, "Olaps Rev " F_U64 "\n", olapsRev); - fprintf(stderr, "Total: "F_U64"\n", Total_Alignments_Ct); - fprintf(stderr, "Failed: "F_U64" (both)\n", Failed_Alignments_Both_Ct); - fprintf(stderr, "Failed: "F_U64" (either)\n", Failed_Alignments_Ct); - fprintf(stderr, "Failed: "F_U64" (match to end)\n", Failed_Alignments_End_Ct); - fprintf(stderr, "Failed: "F_U64" (negative length)\n", Failed_Alignments_Length_Ct); + fprintf(stderr, "Total: " F_U64 "\n", Total_Alignments_Ct); + fprintf(stderr, "Failed: " F_U64 " (both)\n", Failed_Alignments_Both_Ct); + fprintf(stderr, "Failed: " F_U64 " (either)\n", Failed_Alignments_Ct); + fprintf(stderr, "Failed: " F_U64 " (match to end)\n", Failed_Alignments_End_Ct); + fprintf(stderr, "Failed: " F_U64 " (negative length)\n", Failed_Alignments_Length_Ct); fprintf(stderr, "rhaFail %u rhaPass %u\n", rhaFail, rhaPass); } diff --git a/src/overlapErrorAdjustment/correctOverlaps.C b/src/overlapErrorAdjustment/correctOverlaps.C index ec6621065..778c38601 100644 --- a/src/overlapErrorAdjustment/correctOverlaps.C +++ b/src/overlapErrorAdjustment/correctOverlaps.C @@ -151,7 +151,7 @@ main(int argc, char **argv) { // Load the reads for the overlaps we are going to be correcting, and apply corrections to them - fprintf(stderr, "Correcting reads "F_U32" to "F_U32".\n", G->bgnID, G->endID); + fprintf(stderr, "Correcting reads " F_U32 " to " F_U32 ".\n", G->bgnID, G->endID); Correct_Frags(G, gkpStore); @@ -204,7 +204,7 @@ main(int argc, char **argv) { AS_UTL_safeWrite(fp, &G->endID, "hiid", sizeof(int32), 1); AS_UTL_safeWrite(fp, &G->olapsLen, "num", sizeof(uint64), 1); - fprintf(stderr, "--Allocate "F_U64" MB for output error rates.\n", + fprintf(stderr, "--Allocate " F_U64 " MB for output error rates.\n", (sizeof(uint16) * G->olapsLen) >> 20); uint16 *evalue = new uint16 [G->olapsLen]; diff --git a/src/overlapErrorAdjustment/correctOverlaps.H b/src/overlapErrorAdjustment/correctOverlaps.H index ab5e95032..a69d2d533 100644 --- a/src/overlapErrorAdjustment/correctOverlaps.H +++ b/src/overlapErrorAdjustment/correctOverlaps.H @@ -208,7 +208,7 @@ public: void initialize(coParameters *G_, double errorRate) { G = G_; - fprintf(stderr, "-- Allocate "F_U64" MB for Edit_Array pointers.\n", (sizeof(int32 *) * Edit_Array_Max) >> 20); + fprintf(stderr, "-- Allocate " F_U64 " MB for Edit_Array pointers.\n", (sizeof(int32 *) * Edit_Array_Max) >> 20); Edit_Array_Max = 1 + (uint32)(errorRate * AS_MAX_READLEN); Edit_Array_Lazy = new int32 * [Edit_Array_Max]; diff --git a/src/overlapErrorAdjustment/findErrors-Read_Frags.C b/src/overlapErrorAdjustment/findErrors-Read_Frags.C index ab80b55c1..cb489c7b5 100644 --- a/src/overlapErrorAdjustment/findErrors-Read_Frags.C +++ b/src/overlapErrorAdjustment/findErrors-Read_Frags.C @@ -56,7 +56,7 @@ Read_Frags(feParameters *G, uint64 votesLength = 0; uint64 readsLoaded = 0; - fprintf(stderr, "Read_Frags()-- from "F_U32" through "F_U32"\n", + fprintf(stderr, "Read_Frags()-- from " F_U32 " through " F_U32 "\n", G->bgnID, G->endID); for (uint32 curID=G->bgnID; curID<=G->endID; curID++) { @@ -118,6 +118,6 @@ Read_Frags(feParameters *G, delete readData; - fprintf(stderr, "Read_Frags()-- from "F_U32" through "F_U32" -- loaded "F_U64" bases in "F_U64" reads.\n", + fprintf(stderr, "Read_Frags()-- from " F_U32 " through " F_U32 " -- loaded " F_U64 " bases in " F_U64 " reads.\n", G->bgnID, G->endID-1, basesLength, readsLoaded); } diff --git a/src/overlapErrorAdjustment/findErrors-Read_Olaps.C b/src/overlapErrorAdjustment/findErrors-Read_Olaps.C index 8a82a675f..3fa596ed5 100644 --- a/src/overlapErrorAdjustment/findErrors-Read_Olaps.C +++ b/src/overlapErrorAdjustment/findErrors-Read_Olaps.C @@ -37,7 +37,7 @@ Read_Olaps(feParameters *G, gkStore *gkpStore) { uint64 numolaps = ovs->numOverlapsInRange(); - fprintf(stderr, "Read_Olaps()-- loading "F_U64" overlaps.\n", + fprintf(stderr, "Read_Olaps()-- loading " F_U64 " overlaps.\n", numolaps); G->olaps = new Olap_Info_t [numolaps]; diff --git a/src/overlapErrorAdjustment/findErrors.C b/src/overlapErrorAdjustment/findErrors.C index ce47fd5f2..348cb6f0d 100644 --- a/src/overlapErrorAdjustment/findErrors.C +++ b/src/overlapErrorAdjustment/findErrors.C @@ -93,7 +93,7 @@ Extract_Needed_Frags(feParameters *G, assert(loID <= fi); fprintf(stderr, "\n"); - fprintf(stderr, "Extract_Needed_Frags()-- Loading used reads between "F_U32" and "F_U32", at overlap "F_U64".\n", fi, hiID, lastOlap); + fprintf(stderr, "Extract_Needed_Frags()-- Loading used reads between " F_U32 " and " F_U32 ", at overlap " F_U64 ".\n", fi, hiID, lastOlap); while (fi <= hiID) { gkRead *read = gkpStore->gkStore_getRead(fi); @@ -109,7 +109,7 @@ Extract_Needed_Frags(feParameters *G, fi = (lastOlap < G->olapsLen) ? G->olaps[lastOlap].b_iid : hiID + 1; } - fprintf(stderr, "Extract_Needed_Frags()-- Loading reads for overlaps "F_U64" to "F_U64" (reads "F_U32" bases "F_U64")\n", nextOlap, lastOlap, fl->readsLen, fl->basesLen); + fprintf(stderr, "Extract_Needed_Frags()-- Loading reads for overlaps " F_U64 " to " F_U64 " (reads " F_U32 " bases " F_U64 ")\n", nextOlap, lastOlap, fl->readsLen, fl->basesLen); // Ensure there is space. @@ -117,7 +117,7 @@ Extract_Needed_Frags(feParameters *G, delete [] fl->readIDs; delete [] fl->readBases; - //fprintf(stderr, "Extract_Needed_Frags()-- realloc reads from "F_U32" to "F_U32"\n", fl->readsMax, 12 * fl->readsLen / 10); + //fprintf(stderr, "Extract_Needed_Frags()-- realloc reads from " F_U32 " to " F_U32 "\n", fl->readsMax, 12 * fl->readsLen / 10); fl->readIDs = new uint32 [12 * fl->readsLen / 10]; fl->readBases = new char * [12 * fl->readsLen / 10]; @@ -128,7 +128,7 @@ Extract_Needed_Frags(feParameters *G, if (fl->basesMax < fl->basesLen) { delete [] fl->bases; - //fprintf(stderr, "Extract_Needed_Frags()-- realloc bases from "F_U64" to "F_U64"\n", fl->basesMax, 12 * fl->basesLen / 10); + //fprintf(stderr, "Extract_Needed_Frags()-- realloc bases from " F_U64 " to " F_U64 "\n", fl->basesMax, 12 * fl->basesLen / 10); fl->bases = new char [12 * fl->basesLen / 10]; @@ -179,11 +179,11 @@ Extract_Needed_Frags(feParameters *G, fl->readsLen = ii; if (fl->readsLen > 0) - fprintf(stderr, "Extract_Needed_Frags()-- Loaded "F_U32" reads (%.4f%%). Loaded IDs "F_U32" through "F_U32".\n", + fprintf(stderr, "Extract_Needed_Frags()-- Loaded " F_U32 " reads (%.4f%%). Loaded IDs " F_U32 " through " F_U32 ".\n", fl->readsLen, 100.0 * fl->readsLen / (hiID - 1 - loID), fl->readIDs[0], fl->readIDs[fl->readsLen-1]); else - fprintf(stderr, "Extract_Needed_Frags()-- Loaded "F_U32" reads (%.4f%%).\n", + fprintf(stderr, "Extract_Needed_Frags()-- Loaded " F_U32 " reads (%.4f%%).\n", fl->readsLen, 100.0 * fl->readsLen / (hiID - 1 - loID)); } @@ -504,8 +504,8 @@ main(int argc, char **argv) { // All done. Sum up what we did. fprintf(stderr, "\n"); - fprintf(stderr, "Passed overlaps = %10"F_U64P" %8.4f%%\n", passedOlaps, 100.0 * passedOlaps / (failedOlaps + passedOlaps)); - fprintf(stderr, "Failed overlaps = %10"F_U64P" %8.4f%%\n", failedOlaps, 100.0 * failedOlaps / (failedOlaps + passedOlaps)); + fprintf(stderr, "Passed overlaps = %10" F_U64P " %8.4f%%\n", passedOlaps, 100.0 * passedOlaps / (failedOlaps + passedOlaps)); + fprintf(stderr, "Failed overlaps = %10" F_U64P " %8.4f%%\n", failedOlaps, 100.0 * failedOlaps / (failedOlaps + passedOlaps)); // Dump output. diff --git a/src/overlapInCore/overlapInCore-Build_Hash_Index.C b/src/overlapInCore/overlapInCore-Build_Hash_Index.C index e42128a20..a0b3a45d1 100644 --- a/src/overlapInCore/overlapInCore-Build_Hash_Index.C +++ b/src/overlapInCore/overlapInCore-Build_Hash_Index.C @@ -91,7 +91,7 @@ Add_Extra_Hash_String(const char *s) { if (sub >= String_Start_Size) { uint64 n = max(sub * 1.1, String_Start_Size * 1.5); - //fprintf(stderr, "REALLOC String_Start from "F_U64" to "F_U64"\n", String_Start_Size, n); + //fprintf(stderr, "REALLOC String_Start from " F_U64 " to " F_U64 "\n", String_Start_Size, n); resizeArray(String_Start, String_Start_Size, String_Start_Size, n); } @@ -105,7 +105,7 @@ Add_Extra_Hash_String(const char *s) { if (new_len >= Extra_Data_Len) { uint64 n = max(new_len * 1.1, Extra_Data_Len * 1.5); - //fprintf(stderr, "REALLOC basesData from "F_U64" to "F_U64"\n", Extra_Data_Len, n); + //fprintf(stderr, "REALLOC basesData from " F_U64 " to " F_U64 "\n", Extra_Data_Len, n); resizeArray(basesData, Extra_Data_Len, Extra_Data_Len, n); } @@ -280,7 +280,7 @@ Mark_Skip_Kmers(void) { Hash_Mark_Empty (key, line); } - fprintf (stderr, "String_Ct = "F_U64" Extra_String_Ct = "F_U64" Extra_String_Subcount = "F_U64"\n", + fprintf (stderr, "String_Ct = " F_U64 " Extra_String_Ct = " F_U64 " Extra_String_Subcount = " F_U64 "\n", String_Ct, Extra_String_Ct, Extra_String_Subcount); fprintf (stderr, "Read %d kmers to mark to skip\n", ct / 2); } @@ -445,7 +445,7 @@ Build_Hash_Index(gkStore *gkpStore, uint32 bgnID, uint32 endID) { uint64 total_len; uint64 hash_entry_limit; - fprintf(stderr, "Build_Hash_Index from "F_U32" to "F_U32"\n", bgnID, endID); + fprintf(stderr, "Build_Hash_Index from " F_U32 " to " F_U32 "\n", bgnID, endID); Hash_String_Num_Offset = bgnID; String_Ct = 0; @@ -474,10 +474,10 @@ Build_Hash_Index(gkStore *gkpStore, uint32 bgnID, uint32 endID) { hash_entry_limit = G.Max_Hash_Load * HASH_TABLE_SIZE * ENTRIES_PER_BUCKET; #if 0 - fprintf(stderr, "HASH LOADING STARTED: fragID %12"F_U64P"\n", first_frag_id); - fprintf(stderr, "HASH LOADING STARTED: strings %12"F_U64P" out of %12"F_U64P" max.\n", String_Ct, G.Max_Hash_Strings); - fprintf(stderr, "HASH LOADING STARTED: length %12"F_U64P" out of %12"F_U64P" max.\n", total_len, G.Max_Hash_Data_Len); - fprintf(stderr, "HASH LOADING STARTED: entries %12"F_U64P" out of %12"F_U64P" max (load %.2f).\n", Hash_Entries, hash_entry_limit, + fprintf(stderr, "HASH LOADING STARTED: fragID %12" F_U64P "\n", first_frag_id); + fprintf(stderr, "HASH LOADING STARTED: strings %12" F_U64P " out of %12" F_U64P " max.\n", String_Ct, G.Max_Hash_Strings); + fprintf(stderr, "HASH LOADING STARTED: length %12" F_U64P " out of %12" F_U64P " max.\n", total_len, G.Max_Hash_Data_Len); + fprintf(stderr, "HASH LOADING STARTED: entries %12" F_U64P " out of %12" F_U64P " max (load %.2f).\n", Hash_Entries, hash_entry_limit, (100.0 * Hash_Entries) / (HASH_TABLE_SIZE * ENTRIES_PER_BUCKET)); #endif @@ -513,13 +513,13 @@ Build_Hash_Index(gkStore *gkpStore, uint32 bgnID, uint32 endID) { maxAlloc += read->gkRead_sequenceLength() + 1; } - fprintf(stderr, "Found "F_U32" reads with length "F_U64" to load; "F_U32" skipped by being too short; "F_U32" skipped per library restriction\n", + fprintf(stderr, "Found " F_U32 " reads with length " F_U64 " to load; " F_U32 " skipped by being too short; " F_U32 " skipped per library restriction\n", nLoadable, maxAlloc, nShort, nSkipped); // This should be less than what the user requested on the command line if (maxAlloc >= G.Max_Hash_Data_Len + AS_MAX_READLEN) - fprintf(stderr, "maxAlloc = "F_U64" G.Max_Hash_Data_Len = "F_U64" AS_MAX_READLEN = %u\n", maxAlloc, G.Max_Hash_Data_Len, AS_MAX_READLEN); + fprintf(stderr, "maxAlloc = " F_U64 " G.Max_Hash_Data_Len = " F_U64 " AS_MAX_READLEN = %u\n", maxAlloc, G.Max_Hash_Data_Len, AS_MAX_READLEN); assert(maxAlloc < G.Max_Hash_Data_Len + AS_MAX_READLEN); // Allocate space, then fill it. @@ -599,7 +599,7 @@ Build_Hash_Index(gkStore *gkpStore, uint32 bgnID, uint32 endID) { // This was computed ahead of time! if (total_len > maxAlloc) - fprintf(stderr, "total_len="F_U64" len="F_U32" maxAlloc="F_U64"\n", total_len, len, maxAlloc); + fprintf(stderr, "total_len=" F_U64 " len=" F_U32 " maxAlloc=" F_U64 "\n", total_len, len, maxAlloc); assert(total_len <= maxAlloc); // What is Extra_Data_Len? It's set to Data_Len if we would have reallocated here. @@ -607,7 +607,7 @@ Build_Hash_Index(gkStore *gkpStore, uint32 bgnID, uint32 endID) { Put_String_In_Hash(curID, String_Ct); if ((String_Ct % 100000) == 0) - fprintf (stderr, "String_Ct:%12"F_U64P"/%12"F_U32P" totalLen:%12"F_U64P"/%12"F_U64P" Hash_Entries:%12"F_U64P"/%12"F_U64P" Load: %.2f%%\n", + fprintf (stderr, "String_Ct:%12" F_U64P "/%12" F_U32P " totalLen:%12" F_U64P "/%12" F_U64P " Hash_Entries:%12" F_U64P "/%12" F_U64P " Load: %.2f%%\n", String_Ct, G.Max_Hash_Strings, total_len, G.Max_Hash_Data_Len, Hash_Entries, @@ -619,9 +619,9 @@ Build_Hash_Index(gkStore *gkpStore, uint32 bgnID, uint32 endID) { delete readData; - fprintf(stderr, "HASH LOADING STOPPED: strings %12"F_U64P" out of %12"F_U32P" max.\n", String_Ct, G.Max_Hash_Strings); - fprintf(stderr, "HASH LOADING STOPPED: length %12"F_U64P" out of %12"F_U64P" max.\n", total_len, G.Max_Hash_Data_Len); - fprintf(stderr, "HASH LOADING STOPPED: entries %12"F_U64P" out of %12"F_U64P" max (load %.2f).\n", Hash_Entries, hash_entry_limit, + fprintf(stderr, "HASH LOADING STOPPED: strings %12" F_U64P " out of %12" F_U32P " max.\n", String_Ct, G.Max_Hash_Strings); + fprintf(stderr, "HASH LOADING STOPPED: length %12" F_U64P " out of %12" F_U64P " max.\n", total_len, G.Max_Hash_Data_Len); + fprintf(stderr, "HASH LOADING STOPPED: entries %12" F_U64P " out of %12" F_U64P " max (load %.2f).\n", Hash_Entries, hash_entry_limit, 100.0 * Hash_Entries / (HASH_TABLE_SIZE * ENTRIES_PER_BUCKET)); if (String_Ct == 0) { @@ -631,7 +631,7 @@ Build_Hash_Index(gkStore *gkpStore, uint32 bgnID, uint32 endID) { Used_Data_Len = total_len; - //fprintf(stderr, "Extra_Ref_Ct = "F_U64" Max_Extra_Ref_Space = "F_U64"\n", Extra_Ref_Ct, Max_Extra_Ref_Space); + //fprintf(stderr, "Extra_Ref_Ct = " F_U64 " Max_Extra_Ref_Space = " F_U64 "\n", Extra_Ref_Ct, Max_Extra_Ref_Space); if (Extra_Ref_Ct > Max_Extra_Ref_Space) { int32 newSize = (Max_Extra_Ref_Space == 0) ? 16 * 1024 : Max_Extra_Ref_Space * 2; diff --git a/src/overlapInCore/overlapInCore-Find_Overlaps.C b/src/overlapInCore/overlapInCore-Find_Overlaps.C index 77d54671a..0f38f95ad 100644 --- a/src/overlapInCore/overlapInCore-Find_Overlaps.C +++ b/src/overlapInCore/overlapInCore-Find_Overlaps.C @@ -237,15 +237,15 @@ Hash_Find(uint64 Key, int64 Sub, char * S, int64 * Where, int * hi_hits) { int is_empty; H_Ref = Hash_Table [Sub].Entry [i]; - //fprintf(stderr, "Href = Hash_Table %u Entry %u = "F_U64"\n", Sub, i, H_Ref); + //fprintf(stderr, "Href = Hash_Table %u Entry %u = " F_U64 "\n", Sub, i, H_Ref); is_empty = getStringRefEmpty(H_Ref); if (! getStringRefLast(H_Ref) && ! is_empty) { (* Where) = ((uint64)getStringRefStringNum(H_Ref) << OFFSET_BITS) + getStringRefOffset(H_Ref); H_Ref = Extra_Ref_Space [(* Where)]; - //fprintf(stderr, "Href = Extra_Ref_Space "F_U64" = "F_U64"\n", *Where, H_Ref); + //fprintf(stderr, "Href = Extra_Ref_Space " F_U64 " = " F_U64 "\n", *Where, H_Ref); } - //fprintf(stderr, "Href = "F_U64" Get String_Start[ "F_U64" ] + "F_U64"\n", getStringRefStringNum(H_Ref), getStringRefOffset(H_Ref)); + //fprintf(stderr, "Href = " F_U64 " Get String_Start[ " F_U64 " ] + " F_U64 "\n", getStringRefStringNum(H_Ref), getStringRefOffset(H_Ref)); T = basesData + String_Start [getStringRefStringNum(H_Ref)] + getStringRefOffset(H_Ref); if (strncmp (S, T, G.Kmer_Len) == 0) { if (is_empty) { diff --git a/src/overlapInCore/overlapInCore-Process_Overlaps.C b/src/overlapInCore/overlapInCore-Process_Overlaps.C index bb31b266b..406a470ca 100644 --- a/src/overlapInCore/overlapInCore-Process_Overlaps.C +++ b/src/overlapInCore/overlapInCore-Process_Overlaps.C @@ -91,7 +91,7 @@ Process_Overlaps(void *ptr){ WA->Kmer_Hits_Skipped_Ct = 0; WA->Multi_Overlap_Ct = 0; - fprintf(stderr, "Thread %02u processes reads "F_U32"-"F_U32"\n", + fprintf(stderr, "Thread %02u processes reads " F_U32 "-" F_U32 "\n", WA->thread_id, WA->bgnID, WA->endID); for (uint32 fi=WA->bgnID; fi<=WA->endID; fi++) { @@ -135,7 +135,7 @@ Process_Overlaps(void *ptr){ // Write out this block of overlaps, no need to keep them in core! // While we have a mutex, also find the next block of things to process. - fprintf(stderr, "Thread %02u writes reads "F_U32"-"F_U32" ("F_U64" overlaps "F_U64"/"F_U64"/"F_U64" kmer hits with/without overlap/skipped)\n", + fprintf(stderr, "Thread %02u writes reads " F_U32 "-" F_U32 " (" F_U64 " overlaps " F_U64 "/" F_U64 "/" F_U64 " kmer hits with/without overlap/skipped)\n", WA->thread_id, WA->bgnID, WA->endID, WA->overlapsLen, WA->Kmer_Hits_With_Olap_Ct, WA->Kmer_Hits_Without_Olap_Ct, WA->Kmer_Hits_Skipped_Ct); diff --git a/src/overlapInCore/overlapInCore.C b/src/overlapInCore/overlapInCore.C index f8b6694cb..b754dfba2 100644 --- a/src/overlapInCore/overlapInCore.C +++ b/src/overlapInCore/overlapInCore.C @@ -249,11 +249,11 @@ OverlapDriver(void) { fprintf(stderr, "\n"); fprintf(stderr, "Range: %u-%u. Store has %u reads.\n", G.bgnRefID, G.endRefID, gkpStore->gkStore_getNumReads()); - fprintf(stderr, "Chunk: "F_U32" reads/thread -- (G.endRefID="F_U32" - G.bgnRefID="F_U32") / G.Num_PThreads="F_U32" / 8\n", + fprintf(stderr, "Chunk: " F_U32 " reads/thread -- (G.endRefID=" F_U32 " - G.bgnRefID=" F_U32 ") / G.Num_PThreads=" F_U32 " / 8\n", G.perThread, G.endRefID, G.bgnRefID, G.Num_PThreads); fprintf(stderr, "\n"); - fprintf(stderr, "Starting "F_U32"-"F_U32" with "F_U32" per thread\n", G.bgnRefID, G.endRefID, G.perThread); + fprintf(stderr, "Starting " F_U32 "-" F_U32 " with " F_U32 " per thread\n", G.bgnRefID, G.endRefID, G.perThread); fprintf(stderr, "\n"); // Initialize each thread, reset the current position. curRefID and endRefID are updated, this @@ -423,7 +423,7 @@ main(int argc, char **argv) { fprintf(stderr, "* No kmer length supplied; -k needed!\n"), err++; if (G.Max_Hash_Strings > MAX_STRING_NUM) - fprintf(stderr, "Too many strings (--hashstrings), must be less than "F_U64"\n", MAX_STRING_NUM), err++; + fprintf(stderr, "Too many strings (--hashstrings), must be less than " F_U64 "\n", MAX_STRING_NUM), err++; if (G.Outfile_Name == NULL) fprintf (stderr, "ERROR: No output file name specified\n"), err++; @@ -491,22 +491,22 @@ main(int argc, char **argv) { // Log parameters. fprintf(stderr, "\n"); - fprintf(stderr, "STRING_NUM_BITS "F_U32"\n", STRING_NUM_BITS); - fprintf(stderr, "OFFSET_BITS "F_U32"\n", OFFSET_BITS); - fprintf(stderr, "STRING_NUM_MASK "F_U64"\n", STRING_NUM_MASK); - fprintf(stderr, "OFFSET_MASK "F_U64"\n", OFFSET_MASK); - fprintf(stderr, "MAX_STRING_NUM "F_U64"\n", MAX_STRING_NUM); + fprintf(stderr, "STRING_NUM_BITS " F_U32 "\n", STRING_NUM_BITS); + fprintf(stderr, "OFFSET_BITS " F_U32 "\n", OFFSET_BITS); + fprintf(stderr, "STRING_NUM_MASK " F_U64 "\n", STRING_NUM_MASK); + fprintf(stderr, "OFFSET_MASK " F_U64 "\n", OFFSET_MASK); + fprintf(stderr, "MAX_STRING_NUM " F_U64 "\n", MAX_STRING_NUM); fprintf(stderr, "\n"); - fprintf(stderr, "Hash_Mask_Bits "F_U32"\n", G.Hash_Mask_Bits); - fprintf(stderr, "Max_Hash_Strings "F_U32"\n", G.Max_Hash_Strings); - fprintf(stderr, "Max_Hash_Data_Len "F_U64"\n", G.Max_Hash_Data_Len); + fprintf(stderr, "Hash_Mask_Bits " F_U32 "\n", G.Hash_Mask_Bits); + fprintf(stderr, "Max_Hash_Strings " F_U32 "\n", G.Max_Hash_Strings); + fprintf(stderr, "Max_Hash_Data_Len " F_U64 "\n", G.Max_Hash_Data_Len); fprintf(stderr, "Max_Hash_Load %f\n", G.Max_Hash_Load); - fprintf(stderr, "Kmer Length "F_U64"\n", G.Kmer_Len); + fprintf(stderr, "Kmer Length " F_U64 "\n", G.Kmer_Len); fprintf(stderr, "Min Overlap Length %d\n", G.Min_Olap_Len); fprintf(stderr, "Max Error Rate %f\n", G.maxErate); - fprintf(stderr, "Min Kmer Matches "F_U64"\n", G.Filter_By_Kmer_Count); + fprintf(stderr, "Min Kmer Matches " F_U64 "\n", G.Filter_By_Kmer_Count); fprintf(stderr, "\n"); - fprintf(stderr, "Num_PThreads "F_U32"\n", G.Num_PThreads); + fprintf(stderr, "Num_PThreads " F_U32 "\n", G.Num_PThreads); omp_set_num_threads(G.Num_PThreads); @@ -527,16 +527,16 @@ main(int argc, char **argv) { } fprintf(stderr, "\n"); - fprintf(stderr, "HASH_TABLE_SIZE "F_U32"\n", HASH_TABLE_SIZE); - fprintf(stderr, "sizeof(Hash_Bucket_t) "F_SIZE_T"\n", sizeof(Hash_Bucket_t)); - fprintf(stderr, "hash table size: "F_SIZE_T" MB\n", (HASH_TABLE_SIZE * sizeof(Hash_Bucket_t)) >> 20); + fprintf(stderr, "HASH_TABLE_SIZE " F_U32 "\n", HASH_TABLE_SIZE); + fprintf(stderr, "sizeof(Hash_Bucket_t) " F_SIZE_T "\n", sizeof(Hash_Bucket_t)); + fprintf(stderr, "hash table size: " F_SIZE_T " MB\n", (HASH_TABLE_SIZE * sizeof(Hash_Bucket_t)) >> 20); fprintf(stderr, "\n"); Hash_Table = new Hash_Bucket_t [HASH_TABLE_SIZE]; - fprintf(stderr, "check "F_SIZE_T" MB\n", (HASH_TABLE_SIZE * sizeof (Check_Vector_t) >> 20)); - fprintf(stderr, "info "F_SIZE_T" MB\n", (G.Max_Hash_Strings * sizeof (Hash_Frag_Info_t) >> 20)); - fprintf(stderr, "start "F_SIZE_T" MB\n", (G.Max_Hash_Strings * sizeof (int64) >> 20)); + fprintf(stderr, "check " F_SIZE_T " MB\n", (HASH_TABLE_SIZE * sizeof (Check_Vector_t) >> 20)); + fprintf(stderr, "info " F_SIZE_T " MB\n", (G.Max_Hash_Strings * sizeof (Hash_Frag_Info_t) >> 20)); + fprintf(stderr, "start " F_SIZE_T " MB\n", (G.Max_Hash_Strings * sizeof (int64) >> 20)); fprintf(stderr, "\n"); Hash_Check_Array = new Check_Vector_t [HASH_TABLE_SIZE]; @@ -577,15 +577,15 @@ main(int argc, char **argv) { } } - fprintf(stats, " Kmer hits without olaps = "F_S64"\n", Kmer_Hits_Without_Olap_Ct); - fprintf(stats, " Kmer hits with olaps = "F_S64"\n", Kmer_Hits_With_Olap_Ct); - //fprintf(stats, " Kmer hits below %u = "F_S64"\n", G.Filter_By_Kmer_Count, Kmer_Hits_Skipped_Ct); - fprintf(stats, " Multiple overlaps/pair = "F_S64"\n", Multi_Overlap_Ct); - fprintf(stats, " Total overlaps produced = "F_S64"\n", Total_Overlaps); - fprintf(stats, " Contained overlaps = "F_S64"\n", Contained_Overlap_Ct); - fprintf(stats, " Dovetail overlaps = "F_S64"\n", Dovetail_Overlap_Ct); - fprintf(stats, "Rejected by short window = "F_S64"\n", Bad_Short_Window_Ct); - fprintf(stats, " Rejected by long window = "F_S64"\n", Bad_Long_Window_Ct); + fprintf(stats, " Kmer hits without olaps = " F_S64 "\n", Kmer_Hits_Without_Olap_Ct); + fprintf(stats, " Kmer hits with olaps = " F_S64 "\n", Kmer_Hits_With_Olap_Ct); + //fprintf(stats, " Kmer hits below %u = " F_S64 "\n", G.Filter_By_Kmer_Count, Kmer_Hits_Skipped_Ct); + fprintf(stats, " Multiple overlaps/pair = " F_S64 "\n", Multi_Overlap_Ct); + fprintf(stats, " Total overlaps produced = " F_S64 "\n", Total_Overlaps); + fprintf(stats, " Contained overlaps = " F_S64 "\n", Contained_Overlap_Ct); + fprintf(stats, " Dovetail overlaps = " F_S64 "\n", Dovetail_Overlap_Ct); + fprintf(stats, "Rejected by short window = " F_S64 "\n", Bad_Short_Window_Ct); + fprintf(stats, " Rejected by long window = " F_S64 "\n", Bad_Long_Window_Ct); if (stats != stderr) fclose(stats); diff --git a/src/overlapInCore/overlapInCorePartition.C b/src/overlapInCore/overlapInCorePartition.C index 2dfa8836b..737d062ab 100644 --- a/src/overlapInCore/overlapInCorePartition.C +++ b/src/overlapInCore/overlapInCorePartition.C @@ -64,16 +64,16 @@ outputJob(FILE *BAT, uint32 &batchName, uint32 &jobName) { - fprintf(BAT, "%03"F_U32P"\n", batchName); - fprintf(JOB, "%06"F_U32P"\n", jobName); + fprintf(BAT, "%03" F_U32P "\n", batchName); + fprintf(JOB, "%06" F_U32P "\n", jobName); if (maxNumReads == 0) { - fprintf(OPT, "-h "F_U32"-"F_U32" -r "F_U32"-"F_U32"\n", + fprintf(OPT, "-h " F_U32 "-" F_U32 " -r " F_U32 "-" F_U32 "\n", hashBeg, hashEnd, refBeg, refEnd); fprintf(stderr, "HASH %10d-%10d REFR %10d-%10d JOB %d\n", hashBeg, hashEnd, refBeg, refEnd, jobName); } else { - fprintf(OPT, "-h "F_U32"-"F_U32" -r "F_U32"-"F_U32" --hashstrings "F_U32" --hashdatalen "F_U32"\n", + fprintf(OPT, "-h " F_U32 "-" F_U32 " -r " F_U32 "-" F_U32 " --hashstrings " F_U32 " --hashdatalen " F_U32 "\n", hashBeg, hashEnd, refBeg, refEnd, maxNumReads, maxLength); fprintf(stderr, "HASH %10d-%10d REFR %10d-%10d STRINGS %10d BASES %10d JOB %d\n", hashBeg, hashEnd, refBeg, refEnd, maxNumReads, maxLength, jobName); @@ -123,7 +123,7 @@ loadReadLengths(gkStore *gkp, doRef[i] = (libToRef.count(i) == 0) ? false : true; } - fprintf(stderr, "Loading lengths of "F_U32" fragments ("F_SIZE_T"mb)\n", + fprintf(stderr, "Loading lengths of " F_U32 " fragments (" F_SIZE_T "mb)\n", numReads, (numReads * sizeof(uint32)) >> 20); memset(readLen, 0, sizeof(uint32) * (numReads + 1)); @@ -153,7 +153,7 @@ loadReadLengths(gkStore *gkp, } if ((ii % 1048576) == 0) - fprintf(stderr, "Loading lengths at "F_U32" out of "F_U32". H: "F_U32","F_U32" R: "F_U32","F_U32"\n", + fprintf(stderr, "Loading lengths at " F_U32 " out of " F_U32 ". H: " F_U32 "," F_U32 " R: " F_U32 "," F_U32 "\n", ii, numReads, hashMin, hashMax, refMin, refMax); } @@ -199,7 +199,7 @@ partitionFrags(gkStore *gkp, if (refMax > numReads) refMax = numReads; - fprintf(stderr, "Partitioning for hash: "F_U32"-"F_U32" ref: "F_U32","F_U32"\n", + fprintf(stderr, "Partitioning for hash: " F_U32 "-" F_U32 " ref: " F_U32 "," F_U32 "\n", hashMin, hashMax, refMin, refMax); hashBeg = hashMin; @@ -282,7 +282,7 @@ partitionLength(gkStore *gkp, if (refMax > numReads) refMax = numReads; - fprintf(stderr, "Partitioning for hash: "F_U32"-"F_U32" ref: "F_U32","F_U32"\n", + fprintf(stderr, "Partitioning for hash: " F_U32 "-" F_U32 " ref: " F_U32 "," F_U32 "\n", hashMin, hashMax, refMin, refMax); hashBeg = hashMin; @@ -448,8 +448,8 @@ main(int argc, char **argv) { if ((ovlRefBlockLength > 0) && (ovlRefBlockSize > 0)) fprintf(stderr, "ERROR: At most one of -rl and -rs can be non-zero.\n"), exit(1); - fprintf(stderr, "HASH: "F_U64" reads or "F_U64" length.\n", ovlHashBlockSize, ovlHashBlockLength); - fprintf(stderr, "REF: "F_U64" reads or "F_U64" length.\n", ovlRefBlockSize, ovlRefBlockLength); + fprintf(stderr, "HASH: " F_U64 " reads or " F_U64 " length.\n", ovlHashBlockSize, ovlHashBlockLength); + fprintf(stderr, "REF: " F_U64 " reads or " F_U64 " length.\n", ovlRefBlockSize, ovlRefBlockLength); gkStore *gkp = gkStore::gkStore_open(gkpStoreName); uint32 numLibs = gkp->gkStore_getNumLibraries(); @@ -457,12 +457,12 @@ main(int argc, char **argv) { for (set::iterator it=libToHash.begin(); it != libToHash.end(); it++) if (numLibs < *it) - fprintf(stderr, "ERROR: -H "F_U32" is invalid; only "F_U32" libraries in '%s'\n", + fprintf(stderr, "ERROR: -H " F_U32 " is invalid; only " F_U32 " libraries in '%s'\n", *it, numLibs, gkpStoreName), invalidLibs++; for (set::iterator it=libToRef.begin(); it != libToRef.end(); it++) if (numLibs < *it) - fprintf(stderr, "ERROR: -R "F_U32" is invalid; only "F_U32" libraries in '%s'\n", + fprintf(stderr, "ERROR: -R " F_U32 " is invalid; only " F_U32 " libraries in '%s'\n", *it, numLibs, gkpStoreName), invalidLibs++; if ((libToHash.size() > 0) && (libToRef.size() > 0)) { @@ -470,9 +470,9 @@ main(int argc, char **argv) { if ((libToHash.find(lib) == libToHash.end()) && (libToRef.find(lib) == libToRef.end())) { if (checkAllLibUsed == true) - fprintf(stderr, "ERROR: library "F_U32" is not mentioned in either -H or -R.\n", lib), invalidLibs++; + fprintf(stderr, "ERROR: library " F_U32 " is not mentioned in either -H or -R.\n", lib), invalidLibs++; else - fprintf(stderr, "Warning: library "F_U32" is not mentioned in either -H or -R.\n", lib); + fprintf(stderr, "Warning: library " F_U32 " is not mentioned in either -H or -R.\n", lib); } } } diff --git a/src/overlapInCore/overlapReadCache.C b/src/overlapInCore/overlapReadCache.C index 1e88a8845..a322a3afa 100644 --- a/src/overlapInCore/overlapReadCache.C +++ b/src/overlapInCore/overlapReadCache.C @@ -191,7 +191,7 @@ overlapReadCache::purgeReads(void) { while ((memoryLimit < memoryUsed) && (maxAge > 1)) { - fprintf(stderr, "purgeReads()-- used "F_U64"MB limit "F_U64"MB -- purge age "F_U32"\n", memoryUsed >> 20, memoryLimit >> 20, maxAge); + fprintf(stderr, "purgeReads()-- used " F_U64 "MB limit " F_U64 "MB -- purge age " F_U32 "\n", memoryUsed >> 20, memoryLimit >> 20, maxAge); for (uint32 rr=0; rr<=nReads; rr++) { if (maxAge == readAge[rr]) { diff --git a/src/stores/gatekeeperCreate.C b/src/stores/gatekeeperCreate.C index ce7a92c1b..12d77dded 100644 --- a/src/stores/gatekeeperCreate.C +++ b/src/stores/gatekeeperCreate.C @@ -156,7 +156,7 @@ loadFASTA(char *L, // Report errors. if (baseErrors > 0) { - fprintf(errorLog, "read '%s' has "F_U32" invalid base%s. Converted to 'N'.\n", + fprintf(errorLog, "read '%s' has " F_U32 " invalid base%s. Converted to 'N'.\n", H, baseErrors, (baseErrors > 1) ? "s" : ""); nWARNS++; } @@ -261,7 +261,7 @@ loadFASTQ(char *L, } if (baseErrors > 0) { - fprintf(errorLog, "read '%s' has "F_U32" invalid base%s. Converted to 'N'.\n", + fprintf(errorLog, "read '%s' has " F_U32 " invalid base%s. Converted to 'N'.\n", L, baseErrors, (baseErrors > 1) ? "s" : ""); nWARNS++; } @@ -307,7 +307,7 @@ loadFASTQ(char *L, } if (QVerrors > 0) { - fprintf(errorLog, "read '%s' has "F_U32" invalid QV%s. Converted to min or max value.\n", + fprintf(errorLog, "read '%s' has " F_U32 " invalid QV%s. Converted to min or max value.\n", L, QVerrors, (QVerrors > 1) ? "s" : ""); nWARNS++; } @@ -359,7 +359,7 @@ loadReads(gkStore *gkpStore, fprintf(stderr, "\n"); fprintf(stderr, " Loading reads from '%s'\n", fileName); - fprintf(htmlLog, "nam "F_U32" %s\n", gkpFileID, fileName); + fprintf(htmlLog, "nam " F_U32 " %s\n", gkpFileID, fileName); fprintf(htmlLog, "lib preset=N/A"); fprintf(htmlLog, " defaultQV=%u", gkpLibrary->gkLibrary_defaultQV()); @@ -408,7 +408,7 @@ loadReads(gkStore *gkpStore, } else { - fprintf(errorLog, "invalid read header '%.40s%s' in file '%s' at line "F_U64", skipping.\n", + fprintf(errorLog, "invalid read header '%.40s%s' in file '%s' at line " F_U64 ", skipping.\n", L, (strlen(L) > 80) ? "..." : "", fileName, lineNumber); L[0] = 0; nWARNSlocal++; @@ -417,7 +417,7 @@ loadReads(gkStore *gkpStore, // If S[0] isn't nul, we loaded a sequence and need to store it. if (Slen < minReadLength) { - fprintf(errorLog, "read '%s' of length "F_U32" in file '%s' at line "F_U64" is too short, skipping.\n", + fprintf(errorLog, "read '%s' of length " F_U32 " in file '%s' at line " F_U64 " is too short, skipping.\n", H, Slen, fileName, lineNumber); if (isFASTA) { @@ -475,32 +475,32 @@ loadReads(gkStore *gkpStore, // Write status to the screen - fprintf(stderr, " Processed "F_U64" lines.\n", lineNumber); + fprintf(stderr, " Processed " F_U64 " lines.\n", lineNumber); - fprintf(stderr, " Loaded "F_U64" bp from:\n", bLOADEDAlocal + bLOADEDQlocal); + fprintf(stderr, " Loaded " F_U64 " bp from:\n", bLOADEDAlocal + bLOADEDQlocal); if (nFASTAlocal > 0) - fprintf(stderr, " "F_U32" FASTA format reads ("F_U64" bp).\n", nFASTAlocal, bLOADEDAlocal); + fprintf(stderr, " " F_U32 " FASTA format reads (" F_U64 " bp).\n", nFASTAlocal, bLOADEDAlocal); if (nFASTQlocal > 0) - fprintf(stderr, " "F_U32" FASTQ format reads ("F_U64" bp).\n", nFASTQlocal, bLOADEDQlocal); + fprintf(stderr, " " F_U32 " FASTQ format reads (" F_U64 " bp).\n", nFASTQlocal, bLOADEDQlocal); if (nWARNSlocal > 0) - fprintf(stderr, " WARNING: "F_U32" reads issued a warning.\n", nWARNSlocal); + fprintf(stderr, " WARNING: " F_U32 " reads issued a warning.\n", nWARNSlocal); if (nSKIPPEDAlocal > 0) - fprintf(stderr, " WARNING: "F_U32" reads (%0.4f%%) with "F_U64" bp (%0.4f%%) were too short (< "F_U32"bp) and were ignored.\n", + fprintf(stderr, " WARNING: " F_U32 " reads (%0.4f%%) with " F_U64 " bp (%0.4f%%) were too short (< " F_U32 "bp) and were ignored.\n", nSKIPPEDAlocal, 100.0 * nSKIPPEDAlocal / (nSKIPPEDAlocal + nLOADEDAlocal), bSKIPPEDAlocal, 100.0 * bSKIPPEDAlocal / (bSKIPPEDAlocal + bLOADEDAlocal), minReadLength); if (nSKIPPEDQlocal > 0) - fprintf(stderr, " WARNING: "F_U32" reads (%0.4f%%) with "F_U64" bp (%0.4f%%) were too short (< "F_U32"bp) and were ignored.\n", + fprintf(stderr, " WARNING: " F_U32 " reads (%0.4f%%) with " F_U64 " bp (%0.4f%%) were too short (< " F_U32 "bp) and were ignored.\n", nSKIPPEDQlocal, 100.0 * nSKIPPEDQlocal / (nSKIPPEDQlocal + nLOADEDQlocal), bSKIPPEDQlocal, 100.0 * bSKIPPEDQlocal / (bSKIPPEDQlocal + bLOADEDQlocal), minReadLength); // Write status to HTML - fprintf(htmlLog, "dat "F_U32" "F_U64" "F_U32" "F_U64" "F_U32" "F_U64" "F_U32" "F_U64" "F_U32"\n", + fprintf(htmlLog, "dat " F_U32 " " F_U64 " " F_U32 " " F_U64 " " F_U32 " " F_U64 " " F_U32 " " F_U64 " " F_U32 "\n", nLOADEDAlocal, bLOADEDAlocal, nSKIPPEDAlocal, bSKIPPEDAlocal, nLOADEDQlocal, bLOADEDQlocal, @@ -706,18 +706,18 @@ main(int argc, char **argv) { fprintf(stderr, "\n"); fprintf(stderr, "Finished with:\n"); - fprintf(stderr, " "F_U32" warnings (bad base or qv, too short, too long)\n", nWARNS); + fprintf(stderr, " " F_U32 " warnings (bad base or qv, too short, too long)\n", nWARNS); fprintf(stderr, "\n"); fprintf(stderr, "Loaded into store:\n"); - fprintf(stderr, " "F_U64" bp.\n", bLOADED); - fprintf(stderr, " "F_U32" reads.\n", nLOADED); + fprintf(stderr, " " F_U64 " bp.\n", bLOADED); + fprintf(stderr, " " F_U32 " reads.\n", nLOADED); fprintf(stderr, "\n"); fprintf(stderr, "Skipped (too short):\n"); - fprintf(stderr, " "F_U64" bp (%.4f%%).\n", bSKIPPED, 100.0 * bSKIPPED / (bSKIPPED + bLOADED)); - fprintf(stderr, " "F_U32" reads (%.4f%%).\n", nSKIPPED, 100.0 * nSKIPPED / (nSKIPPED + nLOADED)); + fprintf(stderr, " " F_U64 " bp (%.4f%%).\n", bSKIPPED, 100.0 * bSKIPPED / (bSKIPPED + bLOADED)); + fprintf(stderr, " " F_U32 " reads (%.4f%%).\n", nSKIPPED, 100.0 * nSKIPPED / (nSKIPPED + nLOADED)); fprintf(stderr, "\n"); fprintf(stderr, "\n"); - fprintf(htmlLog, "sum "F_U32" "F_U64" "F_U32" "F_U64" "F_U32"\n", nLOADED, bLOADED, nSKIPPED, bSKIPPED, nWARNS); + fprintf(htmlLog, "sum " F_U32 " " F_U64 " " F_U32 " " F_U64 " " F_U32 "\n", nLOADED, bLOADED, nSKIPPED, bSKIPPED, nWARNS); fclose(htmlLog); diff --git a/src/stores/gatekeeperDumpFASTQ.C b/src/stores/gatekeeperDumpFASTQ.C index 054ad7bad..c0bce6e31 100644 --- a/src/stores/gatekeeperDumpFASTQ.C +++ b/src/stores/gatekeeperDumpFASTQ.C @@ -303,7 +303,7 @@ main(int argc, char **argv) { endID = numReads; if (endID < bgnID) - fprintf(stderr, "No reads to dump; reversed ranges make no sense: bgn="F_U32" end="F_U32"??\n", bgnID, endID); + fprintf(stderr, "No reads to dump; reversed ranges make no sense: bgn=" F_U32 " end=" F_U32 "??\n", bgnID, endID); @@ -402,22 +402,22 @@ main(int argc, char **argv) { if (dumpFASTA) // Dear GCC: I'm NOT ambiguous if ((withReadName == true) && (name != NULL)) AS_UTL_writeFastA(out[libID]->getFASTA(), seq, clen, 100, - ">%s id="F_U32" clr="F_U32","F_U32"\n", + ">%s id=" F_U32 " clr=" F_U32 "," F_U32 "\n", name, rid, lclr, rclr); else AS_UTL_writeFastA(out[libID]->getFASTA(), seq, clen, 100, - ">"F_U32" clr="F_U32","F_U32"\n", + ">" F_U32 " clr=" F_U32 "," F_U32 "\n", rid, lclr, rclr); if (dumpFASTQ) // Dear GCC: I'm NOT ambiguous if ((withReadName == true) && (name != NULL)) AS_UTL_writeFastQ(out[libID]->getFASTQ(), seq, clen, qlt, clen, - "@%s id="F_U32" clr="F_U32","F_U32"\n", + "@%s id=" F_U32 " clr=" F_U32 "," F_U32 "\n", name, rid, lclr, rclr); else AS_UTL_writeFastQ(out[libID]->getFASTQ(), seq, clen, qlt, clen, - "@"F_U32" clr="F_U32","F_U32"\n", + "@" F_U32 " clr=" F_U32 "," F_U32 "\n", rid, lclr, rclr); } diff --git a/src/stores/gatekeeperDumpMetaData.C b/src/stores/gatekeeperDumpMetaData.C index 04dd6d9fe..73bc7b31e 100644 --- a/src/stores/gatekeeperDumpMetaData.C +++ b/src/stores/gatekeeperDumpMetaData.C @@ -41,7 +41,7 @@ dumpLibs(gkStore *gkp, uint32 bgnID, uint32 endID) { for (uint32 lid=bgnID; lid<=endID; lid++) { gkLibrary *library = gkp->gkStore_getLibrary(lid); - fprintf(stdout, F_U32"\t"F_U32"\t%s\t%s\t%s\t"F_U32"\t"F_U32"\t"F_U32"\t"F_U32"\t"F_U32"\t%s\n", + fprintf(stdout, F_U32"\t" F_U32 "\t%s\t%s\t%s\t" F_U32 "\t" F_U32 "\t" F_U32 "\t" F_U32 "\t" F_U32 "\t%s\n", library->gkLibrary_libraryID(), library->gkLibrary_isNonRandom(), library->gkLibrary_readTypeString(), @@ -68,12 +68,12 @@ dumpReads(gkStore *gkp, uint32 bgnID, uint32 endID, bool fullDump) { continue; if (fullDump == false) - fprintf(stdout, F_U32"\t"F_U32"\t"F_U32"\n", + fprintf(stdout, F_U32"\t" F_U32 "\t" F_U32 "\n", read->gkRead_readID(), read->gkRead_libraryID(), read->gkRead_sequenceLength()); else - fprintf(stdout, F_U32"\t"F_U32"\t"F_U32"\t"F_U64"\t"F_U64"\n", + fprintf(stdout, F_U32"\t" F_U32 "\t" F_U32 "\t" F_U64 "\t" F_U64 "\n", read->gkRead_readID(), read->gkRead_libraryID(), read->gkRead_sequenceLength(), @@ -147,7 +147,7 @@ dumpStats(gkStore *gkp, uint32 bgnID, uint32 endID) { // length histogram plot for (uint32 l=0; lgkStore_getNumLibraries() + 1; l++) { - fprintf(stdout, "library "F_U32" reads "F_U32" bases: total "F_U64" ave "F_U64" min "F_U64" max "F_U64"\n", + fprintf(stdout, "library " F_U32 " reads " F_U32 " bases: total " F_U64 " ave " F_U64 " min " F_U64 " max " F_U64 "\n", l, rs[l].numberOfReads(), rs[l].numberOfBases(), rs[l].numberOfBases() / rs[l].numberOfReads(), rs[l].minBases(), rs[l].maxBases()); } } @@ -256,7 +256,7 @@ main(int argc, char **argv) { if (endID < bgnID) - fprintf(stderr, "No objects to dump; reversed ranges make no sense: bgn="F_U32" end="F_U32"??\n", bgnID, endID); + fprintf(stderr, "No objects to dump; reversed ranges make no sense: bgn=" F_U32 " end=" F_U32 "??\n", bgnID, endID); if (wantLibs) diff --git a/src/stores/gkStore.C b/src/stores/gkStore.C index 06625db34..4ce8a6702 100644 --- a/src/stores/gkStore.C +++ b/src/stores/gkStore.C @@ -68,7 +68,7 @@ gkRead::gkRead_loadData(gkReadData *readData, uint8 *blob) { char chunk[5]; if ((blob[0] != 'B') && (blob[1] != 'L') && (blob[2] != 'O') && (blob[3] != 'B')) - fprintf(stderr, "Index error in read "F_U32" %c mPtr "F_U64" pID "F_U64" expected BLOB, got %02x %02x %02x %02x '%c%c%c%c'\n", + fprintf(stderr, "Index error in read " F_U32 " %c mPtr " F_U64 " pID " F_U64 " expected BLOB, got %02x %02x %02x %02x '%c%c%c%c'\n", gkRead_readID(), '?', //(_numberOfPartitions == 0) ? 'm' : 'p', _mPtr, _pID, @@ -210,7 +210,7 @@ gkStore::gkStore_stashReadData(gkRead *read, gkReadData *data) { read->_mPtr = AS_UTL_ftell(_blobsFile); read->_pID = _partitionID; // 0 if not partitioned - //fprintf(stderr, "STASH read %u at position "F_SIZE_T"\n", read->gkRead_readID(), AS_UTL_ftell(_blobsFile)); + //fprintf(stderr, "STASH read %u at position " F_SIZE_T "\n", read->gkRead_readID(), AS_UTL_ftell(_blobsFile)); AS_UTL_safeWrite(_blobsFile, data->_blob, @@ -619,27 +619,27 @@ gkStore::gkStore(char const *path, gkStore_mode mode, uint32 partID) { uint32 failed = 0; if (_info.gkLibrarySize != sizeof(gkLibrary)) - failed += fprintf(stderr, "ERROR: gkLibrary size in store = "F_U32", differs from executable = "F_SIZE_T"\n", + failed += fprintf(stderr, "ERROR: gkLibrary size in store = " F_U32 ", differs from executable = " F_SIZE_T "\n", _info.gkLibrarySize, sizeof(gkLibrary)); if (_info.gkReadSize != sizeof(gkRead)) - failed += fprintf(stderr, "ERROR: gkRead size in store = "F_U32", differs from executable = "F_SIZE_T"\n", + failed += fprintf(stderr, "ERROR: gkRead size in store = " F_U32 ", differs from executable = " F_SIZE_T "\n", _info.gkReadSize, sizeof(gkRead)); if (_info.gkMaxLibrariesBits != AS_MAX_LIBRARIES_BITS) - failed += fprintf(stderr, "ERROR: AS_MAX_LIBRARIES_BITS in store = "F_U32", differs from executable = "F_U32"\n", + failed += fprintf(stderr, "ERROR: AS_MAX_LIBRARIES_BITS in store = " F_U32 ", differs from executable = " F_U32 "\n", _info.gkMaxLibrariesBits, AS_MAX_LIBRARIES_BITS); if (_info.gkLibraryNameSize != LIBRARY_NAME_SIZE) - failed += fprintf(stderr, "ERROR: LIBRARY_NAME_SIZE in store = "F_U32", differs from executable = "F_U32"\n", + failed += fprintf(stderr, "ERROR: LIBRARY_NAME_SIZE in store = " F_U32 ", differs from executable = " F_U32 "\n", _info.gkLibraryNameSize, LIBRARY_NAME_SIZE); if (_info.gkMaxReadBits != AS_MAX_READS_BITS) - failed += fprintf(stderr, "ERROR: AS_MAX_READS_BITS in store = "F_U32", differs from executable = "F_U32"\n", + failed += fprintf(stderr, "ERROR: AS_MAX_READS_BITS in store = " F_U32 ", differs from executable = " F_U32 "\n", _info.gkMaxReadBits, AS_MAX_READS_BITS); if (_info.gkMaxReadLenBits != AS_MAX_READLEN_BITS) - failed += fprintf(stderr, "ERROR: AS_MAX_READLEN_BITS in store = "F_U32", differs from executable = "F_U32"\n", + failed += fprintf(stderr, "ERROR: AS_MAX_READLEN_BITS in store = " F_U32 ", differs from executable = " F_U32 "\n", _info.gkMaxReadLenBits, AS_MAX_READLEN_BITS); if (failed) @@ -830,17 +830,17 @@ gkStore::gkStore(char const *path, gkStore_mode mode, uint32 partID) { sprintf(name, "%s/libraries", _storePath); _librariesMMap = new memoryMappedFile (name, memoryMappedFile_readOnly); _libraries = (gkLibrary *)_librariesMMap->get(0); - //fprintf(stderr, " -- openend '%s' at "F_X64"\n", name, _libraries); + //fprintf(stderr, " -- openend '%s' at " F_X64 "\n", name, _libraries); - sprintf(name, "%s/partitions/reads.%04"F_U32P"", _storePath, partID); + sprintf(name, "%s/partitions/reads.%04" F_U32P, _storePath, partID); _readsMMap = new memoryMappedFile (name, memoryMappedFile_readOnly); _reads = (gkRead *)_readsMMap->get(0); - //fprintf(stderr, " -- openend '%s' at "F_X64"\n", name, _reads); + //fprintf(stderr, " -- openend '%s' at " F_X64 "\n", name, _reads); - sprintf(name, "%s/partitions/blobs.%04"F_U32P"", _storePath, partID); + sprintf(name, "%s/partitions/blobs.%04" F_U32P, _storePath, partID); _blobsMMap = new memoryMappedFile (name, memoryMappedFile_readOnly); _blobs = (void *)_blobsMMap->get(0); - //fprintf(stderr, " -- openend '%s' at "F_X64"\n", name, _blobs); + //fprintf(stderr, " -- openend '%s' at " F_X64 "\n", name, _blobs); } // Info only, no access to reads or libraries. @@ -1174,7 +1174,7 @@ gkStore::gkStore_buildPartitions(uint32 *partitionMap) { maxPartition = partitionMap[fi]; } - fprintf(stderr, "Found "F_U32" unpartitioned reads and maximum partition of "F_U32"\n", + fprintf(stderr, "Found " F_U32 " unpartitioned reads and maximum partition of " F_U32 "\n", unPartitioned, maxPartition); // Create the partitions by opening N copies of the data stores, @@ -1257,7 +1257,7 @@ gkStore::gkStore_buildPartitions(uint32 *partitionMap) { if (pi < UINT32_MAX) { #if 0 - fprintf(stderr, "read "F_U32"="F_U32" len "F_U32" -- blob master "F_U64" -- to part "F_U32" new read id "F_U32" blob "F_U64"/"F_U64" -- at readIdx "F_U32"\n", + fprintf(stderr, "read " F_U32 "=" F_U32 " len " F_U32 " -- blob master " F_U64 " -- to part " F_U32 " new read id " F_U32 " blob " F_U64 "/" F_U64 " -- at readIdx " F_U32 "\n", fi, _reads[fi].gkRead_readID(), _reads[fi].gkRead_sequenceLength(), _reads[fi]._mPtr, pi, @@ -1272,7 +1272,7 @@ gkStore::gkStore_buildPartitions(uint32 *partitionMap) { else { #if 0 - fprintf(stderr, "read "F_U32"="F_U32" len "F_U32" -- blob master "F_U64" -- DELETED\n", + fprintf(stderr, "read " F_U32 "=" F_U32 " len " F_U32 " -- blob master " F_U64 " -- DELETED\n", fi, _reads[fi].gkRead_readID(), _reads[fi].gkRead_sequenceLength(), _reads[fi]._mPtr); #endif @@ -1291,7 +1291,7 @@ gkStore::gkStore_buildPartitions(uint32 *partitionMap) { fclose(rIDmF); for (uint32 i=1; i<=maxPartition; i++) { - fprintf(stderr, "partition "F_U32" has "F_U32" reads\n", i, readfileslen[i]); + fprintf(stderr, "partition " F_U32 " has " F_U32 " reads\n", i, readfileslen[i]); errno = 0; diff --git a/src/stores/gkStore.H b/src/stores/gkStore.H index b503e3505..21d954797 100644 --- a/src/stores/gkStore.H +++ b/src/stores/gkStore.H @@ -372,18 +372,18 @@ public: }; void writeInfoAsText(FILE *F) { - fprintf(F, "gkMagic = 0x"F_X64"\n", gkMagic); - fprintf(F, "gkVersion = 0x"F_X64"\n", gkVersion); + fprintf(F, "gkMagic = 0x" F_X64 "\n", gkMagic); + fprintf(F, "gkVersion = 0x" F_X64 "\n", gkVersion); fprintf(F, "\n"); - fprintf(F, "gkLibrarySize = "F_U32"\n", gkLibrarySize); - fprintf(F, "gkReadSize = "F_U32"\n", gkReadSize); - fprintf(F, "gkMaxLibrariesBits = "F_U32"\n", gkMaxLibrariesBits); - fprintf(F, "gkLibraryNameSize = "F_U32"\n", gkLibraryNameSize); - fprintf(F, "gkMaxReadBits = "F_U32"\n", gkMaxReadBits); - fprintf(F, "gkMaxReadLenBits = "F_U32"\n", gkMaxReadLenBits); + fprintf(F, "gkLibrarySize = " F_U32 "\n", gkLibrarySize); + fprintf(F, "gkReadSize = " F_U32 "\n", gkReadSize); + fprintf(F, "gkMaxLibrariesBits = " F_U32 "\n", gkMaxLibrariesBits); + fprintf(F, "gkLibraryNameSize = " F_U32 "\n", gkLibraryNameSize); + fprintf(F, "gkMaxReadBits = " F_U32 "\n", gkMaxReadBits); + fprintf(F, "gkMaxReadLenBits = " F_U32 "\n", gkMaxReadLenBits); fprintf(F, "\n"); - fprintf(F, "numLibraries = "F_U32"\n", numLibraries); - fprintf(F, "numReads = "F_U32"\n", numReads); + fprintf(F, "numLibraries = " F_U32 "\n", numLibraries); + fprintf(F, "numReads = " F_U32 "\n", numReads); }; private: @@ -536,7 +536,7 @@ public: gkRead *gkStore_addEmptyRead(gkLibrary *lib); void gkStore_loadReadData(gkRead *read, gkReadData *readData) { - //fprintf(stderr, "loadReadData()- read "F_U64" thread "F_S32" out of "F_S32"\n", + //fprintf(stderr, "loadReadData()- read " F_U64 " thread " F_S32 " out of " F_S32 "\n", // read->_readID, omp_get_thread_num(), omp_get_max_threads()); if (_blobs) read->gkRead_loadDataFromMMap(readData, _blobs); diff --git a/src/stores/ovOverlap.C b/src/stores/ovOverlap.C index d4b70de50..21f42069f 100644 --- a/src/stores/ovOverlap.C +++ b/src/stores/ovOverlap.C @@ -40,7 +40,7 @@ ovOverlap::toString(char *str, switch (type) { case ovOverlapAsHangs: - sprintf(str, "%10"F_U32P" %10"F_U32P" %c %6"F_S32P" %6"F_U32P" %6"F_S32P" %7.6f%s%s", + sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_S32P " %6" F_U32P " %6" F_S32P " %7.6f%s%s", a_iid, b_iid, flipped() ? 'I' : 'N', a_hang(), span(), b_hang(), @@ -50,7 +50,7 @@ ovOverlap::toString(char *str, break; case ovOverlapAsCoords: - sprintf(str, "%10"F_U32P" %10"F_U32P" %c %6"F_U32P" %6"F_U32P" %6"F_U32P" %6"F_U32P" %6"F_U32P" %7.6f%s", + sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_U32P " %6" F_U32P " %6" F_U32P " %6" F_U32P " %7.6f%s", a_iid, b_iid, flipped() ? 'I' : 'N', span(), @@ -61,7 +61,7 @@ ovOverlap::toString(char *str, break; case ovOverlapAsRaw: - sprintf(str, "%10"F_U32P" %10"F_U32P" %c %6"F_U32P" %6"F_U64P" %6"F_U64P" %6"F_U64P" %6"F_U64P" %7.6f %s %s %s%s", + sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_U64P " %6" F_U64P " %6" F_U64P " %6" F_U64P " %7.6f %s %s %s%s", a_iid, b_iid, flipped() ? 'I' : 'N', span(), @@ -75,7 +75,7 @@ ovOverlap::toString(char *str, break; case ovOverlapAsCompat: - sprintf(str, "%8"F_U32P" %8"F_U32P" %c %6d %6d %5.2f %5.2f%s", + sprintf(str, "%8" F_U32P " %8" F_U32P " %c %6d %6d %5.2f %5.2f%s", a_iid, b_iid, dat.ovl.flipped ? 'I' : 'N', @@ -87,7 +87,7 @@ ovOverlap::toString(char *str, case ovOverlapAsPaf: // miniasm/map expects entries to be separated by tabs // no padding spaces on names we don't confuse read identifiers - sprintf(str, "%"F_U32P"\t%6"F_U32P"\t%6"F_U32P"\t%6"F_U32P"\t%c\t%"F_U32P"\t%6"F_U32P"\t%6"F_U32P"\t%6"F_U32P"\t%6"F_U32P"\t%6"F_U32P"\t%6"F_U32P" %s", + sprintf(str, "%" F_U32P "\t%6" F_U32P "\t%6" F_U32P "\t%6" F_U32P "\t%c\t%" F_U32P "\t%6" F_U32P "\t%6" F_U32P "\t%6" F_U32P "\t%6" F_U32P "\t%6" F_U32P "\t%6" F_U32P " %s", a_iid, (g->gkStore_getRead(a_iid)->gkRead_sequenceLength()), a_bgn(), a_end(), flipped() ? '-' : '+', diff --git a/src/stores/ovStore.C b/src/stores/ovStore.C index 6c44d6e61..729ad530f 100644 --- a/src/stores/ovStore.C +++ b/src/stores/ovStore.C @@ -129,7 +129,7 @@ ovStore::ovStore_read(void) { fclose(ovsinfo); if ((_info._ovsMagic != ovStoreMagic) && (_info._ovsMagic != ovStoreMagicIncomplete)) - fprintf(stderr, "ERROR: directory '%s' is not an overlapStore; magic number 0x%016"F_X64P" incorrect.\n", + fprintf(stderr, "ERROR: directory '%s' is not an overlapStore; magic number 0x%016" F_X64P " incorrect.\n", _storePath, _info._ovsMagic), exit(1); if ((_info._ovsMagic != ovStoreMagic) && (_info._ovsMagic != ovStoreMagicIncomplete)) @@ -137,11 +137,11 @@ ovStore::ovStore_read(void) { _storePath), exit(1); if (_info._ovsVersion != ovStoreVersion) - fprintf(stderr, "ERROR: overlapStore '%s' is version "F_U64"; this code supports only version "F_U64".\n", + fprintf(stderr, "ERROR: overlapStore '%s' is version " F_U64 "; this code supports only version " F_U64 ".\n", _storePath, _info._ovsVersion, ovStoreVersion), exit(1); if (_info._maxReadLenInBits != AS_MAX_READLEN_BITS) - fprintf(stderr, "ERROR: overlapStore '%s' is for AS_MAX_READLEN_BITS="F_U64"; this code supports only %d bits.\n", + fprintf(stderr, "ERROR: overlapStore '%s' is for AS_MAX_READLEN_BITS=" F_U64 "; this code supports only %d bits.\n", _storePath, _info._maxReadLenInBits, AS_MAX_READLEN_BITS), exit(1); // Load stats @@ -264,13 +264,13 @@ ovStore::~ovStore() { fclose(ovsinfo); fprintf(stderr, "Closing the new store:\n"); - fprintf(stderr, " info._ovsMagic = 0x%016"F_X64P"\n", _info._ovsMagic); - fprintf(stderr, " info._ovsVersion = "F_U64"\n", _info._ovsVersion); - fprintf(stderr, " info._smallestIID = "F_U64"\n", _info._smallestIID); - fprintf(stderr, " info._largestIID = "F_U64"\n", _info._largestIID); - fprintf(stderr, " info._numOverlapsTotal = "F_U64"\n", _info._numOverlapsTotal); - fprintf(stderr, " info._highestFileIndex = "F_U64"\n", _info._highestFileIndex); - fprintf(stderr, " info._maxReadLenInBits = "F_U64"\n", _info._maxReadLenInBits); + fprintf(stderr, " info._ovsMagic = 0x%016" F_X64P "\n", _info._ovsMagic); + fprintf(stderr, " info._ovsVersion = " F_U64 "\n", _info._ovsVersion); + fprintf(stderr, " info._smallestIID = " F_U64 "\n", _info._smallestIID); + fprintf(stderr, " info._largestIID = " F_U64 "\n", _info._largestIID); + fprintf(stderr, " info._numOverlapsTotal = " F_U64 "\n", _info._numOverlapsTotal); + fprintf(stderr, " info._highestFileIndex = " F_U64 "\n", _info._highestFileIndex); + fprintf(stderr, " info._maxReadLenInBits = " F_U64 "\n", _info._maxReadLenInBits); } if (_evaluesMap) { @@ -639,8 +639,8 @@ ovStore::writeOverlap(ovOverlap *overlap) { if (_offt._a_iid > overlap->a_iid) { // Woah! The last overlap we saw is bigger than the one we have now?! - fprintf(stderr, "LAST: a:"F_U32"\n", _offt._a_iid); - fprintf(stderr, "THIS: a:"F_U32" b:"F_U32"\n", overlap->a_iid, overlap->b_iid); + fprintf(stderr, "LAST: a:" F_U32 "\n", _offt._a_iid); + fprintf(stderr, "THIS: a:" F_U32 " b:" F_U32 "\n", overlap->a_iid, overlap->b_iid); } assert(_offt._a_iid <= overlap->a_iid); @@ -724,8 +724,8 @@ ovStore::writeOverlap(ovOverlap *overlap, uint32 maxOverlapsThisFile) { for (uint64 i=0; i < maxOverlapsThisFile; i++ ) { // All overlaps will be sorted by a_iid if (_offt._a_iid > overlap[i].a_iid) { - fprintf(stderr, "LAST: a:"F_U32"\n", _offt._a_iid); - fprintf(stderr, "THIS: a:"F_U32" b:"F_U32"\n", overlap[i].a_iid, overlap[i].b_iid); + fprintf(stderr, "LAST: a:" F_U32 "\n", _offt._a_iid); + fprintf(stderr, "THIS: a:" F_U32 " b:" F_U32 "\n", overlap[i].a_iid, overlap[i].b_iid); } assert(_offt._a_iid <= overlap[i].a_iid); @@ -841,7 +841,7 @@ ovStore::numOverlapsPerFrag(uint32 &firstFrag, uint32 &lastFrag) { uint64 act = AS_UTL_safeRead(_offtFile, offsets, "ovStore::numOverlapsInRange::offsets", sizeof(ovStoreOfft), len); if (len != act) - fprintf(stderr, "AS_OVS_numOverlapsPerFrag()-- short read on offsets! Expected len="F_U64" read act="F_U64"\n", len, act), exit(1); + fprintf(stderr, "AS_OVS_numOverlapsPerFrag()-- short read on offsets! Expected len=" F_U64 " read act=" F_U64 "\n", len, act), exit(1); for (uint64 i=0; iwriteOverlap(ovls + i); if (offt._a_iid > ovls[i].a_iid) { - fprintf(stderr, "LAST: a:"F_U32"\n", offt._a_iid); - fprintf(stderr, "THIS: a:"F_U32" b:"F_U32"\n", ovls[i].a_iid, ovls[i].b_iid); + fprintf(stderr, "LAST: a:" F_U32 "\n", offt._a_iid); + fprintf(stderr, "THIS: a:" F_U32 " b:" F_U32 "\n", ovls[i].a_iid, ovls[i].b_iid); } assert(offt._a_iid <= ovls[i].a_iid); @@ -1093,9 +1093,9 @@ writeOverlaps(char *storePath, fclose(F); - fprintf(stderr, "Wrote "F_U64" overlaps into '%s'\n", info._numOverlapsTotal, name); - fprintf(stderr, " Smallest "F_U64"\n", info._smallestIID); - fprintf(stderr, " Largest "F_U64"\n", info._largestIID); + fprintf(stderr, "Wrote " F_U64 " overlaps into '%s'\n", info._numOverlapsTotal, name); + fprintf(stderr, " Smallest " F_U64 "\n", info._smallestIID); + fprintf(stderr, " Largest " F_U64 "\n", info._largestIID); } @@ -1150,16 +1150,16 @@ testIndex(char *ovlName, maxIID = O._a_iid; if (errorDecreased) - fprintf(stderr, "ERROR: index decreased from "F_U32" to "F_U32"\n", curIID, O._a_iid), nErrs++; + fprintf(stderr, "ERROR: index decreased from " F_U32 " to " F_U32 "\n", curIID, O._a_iid), nErrs++; else if (errorGap) - fprintf(stderr, "ERROR: gap between "F_U32" and "F_U32"\n", curIID, O._a_iid), nErrs++; + fprintf(stderr, "ERROR: gap between " F_U32 " and " F_U32 "\n", curIID, O._a_iid), nErrs++; if ((maxIncreases == true) && (errorGap == false)) { if (doFixes) AS_UTL_safeWrite(F, &O, "offset", sizeof(ovStoreOfft), 1); } else if (O._numOlaps > 0) { - fprintf(stderr, "ERROR: lost overlaps a_iid "F_U32" fileno "F_U32" offset "F_U32" numOlaps "F_U32"\n", + fprintf(stderr, "ERROR: lost overlaps a_iid " F_U32 " fileno " F_U32 " offset " F_U32 " numOlaps " F_U32 "\n", O._a_iid, O._fileno, O._offset, O._numOlaps); } @@ -1253,7 +1253,7 @@ mergeInfoFiles(char *storePath, assert(infopiece._smallestIID <= infopiece._largestIID); if (info._largestIID + 1 < infopiece._smallestIID) - fprintf(stderr, " Adding empty records for fragments "F_U64" to "F_U64"\n", + fprintf(stderr, " Adding empty records for fragments " F_U64 " to " F_U64 "\n", info._largestIID + 1, infopiece._smallestIID - 1); while (info._largestIID + 1 < infopiece._smallestIID) { @@ -1286,7 +1286,7 @@ mergeInfoFiles(char *storePath, if (recsLen > 0) { if (info._largestIID + 1 != recs[0]._a_iid) - fprintf(stderr, "ERROR: '%s' starts with iid "F_U32", but store only up to "F_U64"\n", + fprintf(stderr, "ERROR: '%s' starts with iid " F_U32 ", but store only up to " F_U64 "\n", name, recs[0]._a_iid, info._largestIID); assert(info._largestIID + 1 == recs[0]._a_iid); } @@ -1328,7 +1328,7 @@ mergeInfoFiles(char *storePath, info._numOverlapsTotal += infopiece._numOverlapsTotal; - fprintf(stderr, " Now finished with fragments "F_U64" to "F_U64" -- "F_U64" overlaps.\n", + fprintf(stderr, " Now finished with fragments " F_U64 " to " F_U64 " -- " F_U64 " overlaps.\n", info._smallestIID, info._largestIID, info._numOverlapsTotal); } @@ -1351,7 +1351,7 @@ mergeInfoFiles(char *storePath, } fprintf(stderr, "\n"); - fprintf(stderr, "Index finalized for reads "F_U64" to "F_U64" with "F_U64" overlaps.\n", + fprintf(stderr, "Index finalized for reads " F_U64 " to " F_U64 " with " F_U64 " overlaps.\n", info._smallestIID, info._largestIID, info._numOverlapsTotal); @@ -1426,7 +1426,7 @@ ovStoreFilter::filterOverlap(ovOverlap &foverlap, (foverlap.b_iid >= maxID)) { char ovlstr[256]; - fprintf(stderr, "Overlap has IDs out of range (maxID "F_U32"), possibly corrupt input data.\n", maxID); + fprintf(stderr, "Overlap has IDs out of range (maxID " F_U32 "), possibly corrupt input data.\n", maxID); fprintf(stderr, " coords -- %s\n", foverlap.toString(ovlstr, ovOverlapAsCoords, false)); fprintf(stderr, " hangs -- %s\n", foverlap.toString(ovlstr, ovOverlapAsHangs, false)); exit(1); @@ -1561,19 +1561,19 @@ ovStoreFilter::filterOverlap(ovOverlap &foverlap, void ovStoreFilter::reportFate(void) { fprintf(stderr, "overlap fate:\n"); - fprintf(stderr, "%16"F_U64P" SAVE - overlaps output (for unitigging)\n", saveUTG); - fprintf(stderr, "%16"F_U64P" SAVE - overlaps output (for OBT)\n", saveOBT); - fprintf(stderr, "%16"F_U64P" SAVE - overlaps output (for dedupe)\n", saveDUP); + fprintf(stderr, "%16" F_U64P " SAVE - overlaps output (for unitigging)\n", saveUTG); + fprintf(stderr, "%16" F_U64P " SAVE - overlaps output (for OBT)\n", saveOBT); + fprintf(stderr, "%16" F_U64P " SAVE - overlaps output (for dedupe)\n", saveDUP); fprintf(stderr, "\n"); - fprintf(stderr, "%16"F_U64P" ERATE - low quality, more than %.3f fraction error\n", skipERATE, AS_OVS_decodeEvalue(maxEvalue)); + fprintf(stderr, "%16" F_U64P " ERATE - low quality, more than %.3f fraction error\n", skipERATE, AS_OVS_decodeEvalue(maxEvalue)); fprintf(stderr, "\n"); - fprintf(stderr, "%16"F_U64P" OBT - not requested\n", skipOBT); - fprintf(stderr, "%16"F_U64P" OBT - too similar\n", skipOBTbad); - fprintf(stderr, "%16"F_U64P" OBT - too short\n", skipOBTshort); + fprintf(stderr, "%16" F_U64P " OBT - not requested\n", skipOBT); + fprintf(stderr, "%16" F_U64P " OBT - too similar\n", skipOBTbad); + fprintf(stderr, "%16" F_U64P " OBT - too short\n", skipOBTshort); fprintf(stderr, "\n"); - fprintf(stderr, "%16"F_U64P" DUP - dedupe not requested\n", skipDUP); - fprintf(stderr, "%16"F_U64P" DUP - different library\n", skipDUPlib); - fprintf(stderr, "%16"F_U64P" DUP - obviously not duplicates\n", skipDUPdiff); + fprintf(stderr, "%16" F_U64P " DUP - dedupe not requested\n", skipDUP); + fprintf(stderr, "%16" F_U64P " DUP - different library\n", skipDUPlib); + fprintf(stderr, "%16" F_U64P " DUP - obviously not duplicates\n", skipDUPdiff); } diff --git a/src/stores/ovStore.H b/src/stores/ovStore.H index a33f28f0a..62e1ce9fe 100644 --- a/src/stores/ovStore.H +++ b/src/stores/ovStore.H @@ -648,7 +648,7 @@ public: } } - fprintf(stderr, "Marked "F_U32" reads so skip OBT, "F_U32" reads to skip dedupe.\n", numSkipOBT, numSkipDUP); + fprintf(stderr, "Marked " F_U32 " reads so skip OBT, " F_U32 " reads to skip dedupe.\n", numSkipOBT, numSkipDUP); }; ~ovStoreFilter() { diff --git a/src/stores/ovStoreBucketizer.C b/src/stores/ovStoreBucketizer.C index 9601ccb0d..bd6e49f21 100644 --- a/src/stores/ovStoreBucketizer.C +++ b/src/stores/ovStoreBucketizer.C @@ -172,7 +172,7 @@ main(int argc, char **argv) { if (jobIndex == 0) fprintf(stderr, "ERROR: No job index (-job) supplied.\n"); if (fileLimit > maxFiles) - fprintf(stderr, "ERROR: Too many jobs (-F); only "F_U32" supported on this architecture.\n", maxFiles); + fprintf(stderr, "ERROR: Too many jobs (-F); only " F_U32 " supported on this architecture.\n", maxFiles); exit(1); } @@ -223,7 +223,7 @@ main(int argc, char **argv) { AS_UTL_safeRead(C, iidToBucket, "iidToBucket", sizeof(uint32), maxIID); if (maxIIDtest != maxIID) - fprintf(stderr, "ERROR: maxIID in store ("F_U32") differs from maxIID in config file ("F_U32").\n", + fprintf(stderr, "ERROR: maxIID in store (" F_U32 ") differs from maxIID in config file (" F_U32 ").\n", maxIID, maxIIDtest), exit(1); } @@ -234,7 +234,7 @@ main(int argc, char **argv) { memset(sliceFile, 0, sizeof(ovFile *) * (fileLimit + 1)); memset(sliceSize, 0, sizeof(uint64) * (fileLimit + 1)); - fprintf(stderr, "maxError fraction: %.3f percent: %.3f encoded: "F_U64"\n", + fprintf(stderr, "maxError fraction: %.3f percent: %.3f encoded: " F_U64 "\n", maxErrorRate, maxErrorRate * 100, maxError); fprintf(stderr, "Bucketizing %s\n", ovlInput); diff --git a/src/stores/ovStoreBuild.C b/src/stores/ovStoreBuild.C index bb7a646eb..48109be85 100644 --- a/src/stores/ovStoreBuild.C +++ b/src/stores/ovStoreBuild.C @@ -173,7 +173,7 @@ computeIIDperBucket(uint32 fileLimit, exit(1); } - fprintf(stderr, "Found "F_U64" (%.2f million) overlaps.\n", numOverlaps, numOverlaps / 1000000.0); + fprintf(stderr, "Found " F_U64 " (%.2f million) overlaps.\n", numOverlaps, numOverlaps / 1000000.0); // Partition the overlaps into buckets. @@ -183,7 +183,7 @@ computeIIDperBucket(uint32 fileLimit, // If a file limit, distribute the overlaps to equal sized files. if (fileLimit > 0) { olapsPerBucketMax = (uint64)ceil((double)numOverlaps / (double)fileLimit); - fprintf(stderr, "Will sort using "F_U32" files; "F_U64" (%.2f million) overlaps per bucket; %.2f GB memory per bucket\n", + fprintf(stderr, "Will sort using " F_U32 " files; " F_U64 " (%.2f million) overlaps per bucket; %.2f GB memory per bucket\n", fileLimit, olapsPerBucketMax, olapsPerBucketMax / 1000000.0, olapsPerBucketMax * GBperOlap); } @@ -193,13 +193,13 @@ computeIIDperBucket(uint32 fileLimit, // values can break this - either too low memory or too high allowed open files (an OS limit). if (maxMemory > 0) { - fprintf(stderr, "Configuring for %.2f GB to %.2f GB memory and "F_S64" open files.\n", + fprintf(stderr, "Configuring for %.2f GB to %.2f GB memory and " F_S64 " open files.\n", minMemory / 1024.0 / 1024.0 / 1024.0, maxMemory / 1024.0 / 1024.0 / 1024.0, maxFiles); if (minMemory < MEMORY_OVERHEAD + ovOverlapSortSize) { - fprintf(stderr, "Reset minMemory from "F_U64" to "F_U64"\n", minMemory, MEMORY_OVERHEAD + ovOverlapSortSize); + fprintf(stderr, "Reset minMemory from " F_U64 " to " F_U64 "\n", minMemory, MEMORY_OVERHEAD + ovOverlapSortSize); minMemory = MEMORY_OVERHEAD + ovOverlapSortSize; } @@ -215,7 +215,7 @@ computeIIDperBucket(uint32 fileLimit, ((useMemory <= maxMemory) && (numOverlaps / olapsPerBucketMax + 1 > maxFiles)); useMemory += incr) { olapsPerBucketMax = (useMemory - MEMORY_OVERHEAD) / ovOverlapSortSize; - fprintf(stderr, "At memory %.3fGB, "F_U64" olaps per bucket, "F_U64" buckets (pass 1).\n", + fprintf(stderr, "At memory %.3fGB, " F_U64 " olaps per bucket, " F_U64 " buckets (pass 1).\n", useMemory / 1024.0 / 1024.0 / 1024.0, olapsPerBucketMax, numOverlaps / olapsPerBucketMax + 1); } @@ -227,7 +227,7 @@ computeIIDperBucket(uint32 fileLimit, ((useMemory <= maxMemory) && (numOverlaps / olapsPerBucketMax + 1 > maxFiles / 2)); useMemory += incr) { olapsPerBucketMax = (useMemory - MEMORY_OVERHEAD) / ovOverlapSortSize; - fprintf(stderr, "At memory %.3fGB, "F_U64" olaps per bucket, "F_U64" buckets (pass 2).\n", + fprintf(stderr, "At memory %.3fGB, " F_U64 " olaps per bucket, " F_U64 " buckets (pass 2).\n", useMemory / 1024.0 / 1024.0 / 1024.0, olapsPerBucketMax, numOverlaps / olapsPerBucketMax + 1); } } @@ -239,17 +239,17 @@ computeIIDperBucket(uint32 fileLimit, fprintf(stderr, "ERROR: Cannot sort %.2f million overlaps using %.2f GB memory; too few file handles available.\n", numOverlaps / 1000000.0, maxMemory / 1024.0 / 1024.0 / 1024.0); - fprintf(stderr, "ERROR: minMemory "F_U64"\n", minMemory); - fprintf(stderr, "ERROR: maxMemory "F_U64"\n", maxMemory); - fprintf(stderr, "ERROR: olapsPerBucket "F_U64"\n", olapsPerBucketMax); - fprintf(stderr, "ERROR: buckets "F_U64"\n", numOverlaps / olapsPerBucketMax + 1); - fprintf(stderr, "ERROR: SC_CHILD_MAX "F_S64"\n", sysconf(_SC_CHILD_MAX)); - fprintf(stderr, "ERROR: SC_OPEN_MAX "F_S64"\n", sysconf(_SC_OPEN_MAX)); + fprintf(stderr, "ERROR: minMemory " F_U64 "\n", minMemory); + fprintf(stderr, "ERROR: maxMemory " F_U64 "\n", maxMemory); + fprintf(stderr, "ERROR: olapsPerBucket " F_U64 "\n", olapsPerBucketMax); + fprintf(stderr, "ERROR: buckets " F_U64 "\n", numOverlaps / olapsPerBucketMax + 1); + fprintf(stderr, "ERROR: SC_CHILD_MAX " F_S64 "\n", sysconf(_SC_CHILD_MAX)); + fprintf(stderr, "ERROR: SC_OPEN_MAX " F_S64 "\n", sysconf(_SC_OPEN_MAX)); fprintf(stderr, "ERROR: Increase memory size (in canu, ovsMemory; in ovStoreBuild, -M)\n"); exit(1); } - fprintf(stderr, "Will sort using "F_U64" files; "F_U64" (%.2f million) overlaps per bucket; %.2f GB memory per bucket\n", + fprintf(stderr, "Will sort using " F_U64 " files; " F_U64 " (%.2f million) overlaps per bucket; %.2f GB memory per bucket\n", numOverlaps / olapsPerBucketMax + 1, olapsPerBucketMax, olapsPerBucketMax / 1000000.0, @@ -287,13 +287,13 @@ computeIIDperBucket(uint32 fileLimit, iidToBucket[ii] = bucket; if (olaps >= olapsPerBucketMax) { - fprintf(stderr, " bucket %3d has "F_U64" olaps.\n", bucket, olaps); + fprintf(stderr, " bucket %3d has " F_U64 " olaps.\n", bucket, olaps); olaps = 0; bucket++; } } - fprintf(stderr, " bucket %3d has "F_U64" olaps.\n", bucket, olaps); + fprintf(stderr, " bucket %3d has " F_U64 " olaps.\n", bucket, olaps); } fprintf(stderr, "Will sort %.3f million overlaps per bucket, using %u buckets %.2f GB per bucket.\n", @@ -434,9 +434,9 @@ main(int argc, char **argv) { fprintf(stderr, " -config out.dat don't build a store, just dump a binary partitioning file for ovStoreBucketizer\n"); fprintf(stderr, "\n"); fprintf(stderr, "Sizes and Limits:\n"); - fprintf(stderr, " ovOverlapSortSize "F_U64" bytes\n", ovOverlapSortSize); - fprintf(stderr, " SC_CHILD_MAX "F_U64" processes\n", sysconf(_SC_CHILD_MAX)); - fprintf(stderr, " SC_OPEN_MAX "F_U64" files\n", sysconf(_SC_OPEN_MAX)); + fprintf(stderr, " ovOverlapSortSize " F_U64 " bytes\n", ovOverlapSortSize); + fprintf(stderr, " SC_CHILD_MAX " F_U64 " processes\n", sysconf(_SC_CHILD_MAX)); + fprintf(stderr, " SC_OPEN_MAX " F_U64 " files\n", sysconf(_SC_OPEN_MAX)); fprintf(stderr, "\n"); if (ovlName == NULL) @@ -446,7 +446,7 @@ main(int argc, char **argv) { if (fileList.size() == 0) fprintf(stderr, "ERROR: No input overlap files (-L or last on the command line) supplied.\n"); if (fileLimit > sysconf(_SC_OPEN_MAX) - 16) - fprintf(stderr, "ERROR: Too many jobs (-F); only "F_SIZE_T" supported on this architecture.\n", sysconf(_SC_OPEN_MAX) - 16); + fprintf(stderr, "ERROR: Too many jobs (-F); only " F_SIZE_T " supported on this architecture.\n", sysconf(_SC_OPEN_MAX) - 16); if (maxMemory < MEMORY_OVERHEAD) fprintf(stderr, "ERROR: Memory (-M) must be at least %.3f GB to account for overhead.\n", MEMORY_OVERHEAD / 1024.0 / 1024.0 / 1024.0); @@ -481,7 +481,7 @@ main(int argc, char **argv) { fclose(fp); - fprintf(stderr, "loading evalues from '%s' -- ID range "F_U32"-"F_U32" with "F_U64" overlaps\n", + fprintf(stderr, "loading evalues from '%s' -- ID range " F_U32 "-" F_U32 " with " F_U64 " overlaps\n", fileList[i], bgnID, endID, len); ovs->addEvalues(bgnID, endID, evalues, len); @@ -506,8 +506,8 @@ main(int argc, char **argv) { if (iidToBucket[maxIID-1] > maxFiles - 8) { fprintf(stderr, "ERROR:\n"); - fprintf(stderr, "ERROR: Operating system limit of "F_U32" open files. The current -F/-M settings\n", maxFiles); - fprintf(stderr, "ERROR: will need to create "F_U32" files to construct the store.\n", iidToBucket[maxIID-1]); + fprintf(stderr, "ERROR: Operating system limit of " F_U32 " open files. The current -F/-M settings\n", maxFiles); + fprintf(stderr, "ERROR: will need to create " F_U32 " files to construct the store.\n", iidToBucket[maxIID-1]); fprintf(stderr, "ERROR:\n"); exit(1); } @@ -643,8 +643,8 @@ main(int argc, char **argv) { (overlapsort[numOvl].b_iid >= maxIID)) { char ovlstr[256]; - fprintf(stderr, "Overlap has IDs out of range (maxIID "F_U64"), possibly corrupt input data.\n", maxIID); - fprintf(stderr, " Aid "F_U32" Bid "F_U32"\n", overlapsort[numOvl].a_iid, overlapsort[numOvl].b_iid); + fprintf(stderr, "Overlap has IDs out of range (maxIID " F_U64 "), possibly corrupt input data.\n", maxIID); + fprintf(stderr, " Aid " F_U32 " Bid " F_U32 "\n", overlapsort[numOvl].a_iid, overlapsort[numOvl].b_iid); exit(1); } diff --git a/src/stores/ovStoreDump.C b/src/stores/ovStoreDump.C index 853d7ec1d..969b9aae9 100644 --- a/src/stores/ovStoreDump.C +++ b/src/stores/ovStoreDump.C @@ -565,7 +565,7 @@ dumpPicture(ovStore *ovlStore, uint32 qryID, char *bestPrefix) { - //fprintf(stderr, "DUMPING PICTURE for ID "F_U32" in store %s (gkp %s)\n", + //fprintf(stderr, "DUMPING PICTURE for ID " F_U32 " in store %s (gkp %s)\n", // qryID, ovlName, gkpName); uint32 Aid = qryID; diff --git a/src/stores/ovStoreFile.C b/src/stores/ovStoreFile.C index 156dd2ef6..e7f2080ef 100644 --- a/src/stores/ovStoreFile.C +++ b/src/stores/ovStoreFile.C @@ -184,7 +184,7 @@ ovFile::~ovFile() { delete [] _olapsPerRead; - //fprintf(stderr, "Wrote counts file '%s' for reads up to iid "F_U32"\n", name, _olapsPerReadLast); + //fprintf(stderr, "Wrote counts file '%s' for reads up to iid " F_U32 "\n", name, _olapsPerReadLast); } } @@ -392,7 +392,7 @@ ovFile::readBuffer(void) { size_t sbc = AS_UTL_safeRead(_file, _snappyBuffer, "ovFile::readBuffer::sb", sizeof(char), cl); if (sbc != cl) - fprintf(stderr, "ERROR: short read on file '%s': read "F_SIZE_T" bytes, expected "F_SIZE_T".\n", + fprintf(stderr, "ERROR: short read on file '%s': read " F_SIZE_T " bytes, expected " F_SIZE_T ".\n", _prefix, sbc, cl), exit(1); size_t ol = 0; diff --git a/src/stores/ovStoreIndexer.C b/src/stores/ovStoreIndexer.C index 328969c25..d65d71439 100644 --- a/src/stores/ovStoreIndexer.C +++ b/src/stores/ovStoreIndexer.C @@ -133,26 +133,26 @@ main(int argc, char **argv) { if (AS_UTL_fileExists(name, FALSE, FALSE) == true) complete++; else - fprintf(stderr, "ERROR: Segment "F_U32" data not present (%s)\n", i, name); + fprintf(stderr, "ERROR: Segment " F_U32 " data not present (%s)\n", i, name); sprintf(name, "%s/%04d.info", ovlName, i); if (AS_UTL_fileExists(name, FALSE, FALSE) == true) complete++; else - fprintf(stderr, "ERROR: Segment "F_U32" info not present (%s)\n", i, name); + fprintf(stderr, "ERROR: Segment " F_U32 " info not present (%s)\n", i, name); sprintf(name, "%s/%04d.index", ovlName, i); if (AS_UTL_fileExists(name, FALSE, FALSE) == true) complete++; else - fprintf(stderr, "ERROR: Segment "F_U32" index not present (%s)\n", i, name); + fprintf(stderr, "ERROR: Segment " F_U32 " index not present (%s)\n", i, name); if (complete == 3) cntJob++; } if (cntJob != maxJob) { - fprintf(stderr, "ERROR: Expected "F_U32" segments, only found "F_U32".\n", maxJob, cntJob); + fprintf(stderr, "ERROR: Expected " F_U32 " segments, only found " F_U32 ".\n", maxJob, cntJob); exit(1); } diff --git a/src/stores/ovStoreSorter.C b/src/stores/ovStoreSorter.C index a911c139c..95f602e90 100644 --- a/src/stores/ovStoreSorter.C +++ b/src/stores/ovStoreSorter.C @@ -155,7 +155,7 @@ main(int argc, char **argv) { sprintf(name,"%s/%04d.ovs", storePath, fileID); if ((forceRun == false) && (AS_UTL_fileExists(name, FALSE, FALSE))) - fprintf(stderr, "Job "F_U32" is running or finished (remove '%s' or -force to try again).\n", fileID, name), exit(0); + fprintf(stderr, "Job " F_U32 " is running or finished (remove '%s' or -force to try again).\n", fileID, name), exit(0); errno = 0; FILE *F = fopen(name, "w"); @@ -201,11 +201,11 @@ main(int argc, char **argv) { if (nr != fileLimit + 1) { fprintf(stderr, "ERROR: short read on '%s'.\n", name); - fprintf(stderr, "ERROR: read "F_U64" sizes insteadof "F_U32".\n", nr, fileLimit + 1); + fprintf(stderr, "ERROR: read " F_U64 " sizes insteadof " F_U32 ".\n", nr, fileLimit + 1); } assert(nr == fileLimit + 1); - fprintf(stderr, "Found "F_U64" overlaps from '%s'.\n", sliceSizes[fileID], name); + fprintf(stderr, "Found " F_U64 " overlaps from '%s'.\n", sliceSizes[fileID], name); bucketSizes[i] = sliceSizes[fileID]; totOvl += sliceSizes[fileID]; @@ -215,7 +215,7 @@ main(int argc, char **argv) { sliceSizes = NULL; if (ovOverlapSortSize * totOvl > maxMemory) { - fprintf(stderr, "ERROR: Overlaps need %.2f GB memory, but process limited (via -M) to "F_U64" GB.\n", + fprintf(stderr, "ERROR: Overlaps need %.2f GB memory, but process limited (via -M) to " F_U64 " GB.\n", ovOverlapSortSize * totOvl / 1024.0 / 1024.0 / 1024.0, maxMemory >> 30); char name[FILENAME_MAX]; @@ -226,7 +226,7 @@ main(int argc, char **argv) { exit(1); } - fprintf(stderr, "Overlaps need %.2f GB memory, allowed to use up to (via -M) "F_U64" GB.\n", + fprintf(stderr, "Overlaps need %.2f GB memory, allowed to use up to (via -M) " F_U64 " GB.\n", ovOverlapSortSize * totOvl / 1024.0 / 1024.0 / 1024.0, maxMemory >> 30); ovOverlap *ovls = ovOverlap::allocateOverlaps(NULL, totOvl); @@ -245,10 +245,10 @@ main(int argc, char **argv) { sprintf(name, "%s/bucket%04d/slice%03d", storePath, i, fileID); if (AS_UTL_fileExists(name, FALSE, FALSE) == false) - fprintf(stderr, "ERROR: "F_U64" overlaps claim to exist in bucket '%s', but file not found.\n", + fprintf(stderr, "ERROR: " F_U64 " overlaps claim to exist in bucket '%s', but file not found.\n", bucketSizes[i], name); - fprintf(stderr, "Loading "F_U64" overlaps from '%s'.\n", bucketSizes[i], name); + fprintf(stderr, "Loading " F_U64 " overlaps from '%s'.\n", bucketSizes[i], name); ovFile *bof = new ovFile(name, ovFileFull); uint64 num = 0; @@ -259,14 +259,14 @@ main(int argc, char **argv) { } if (num != bucketSizes[i]) - fprintf(stderr, "ERROR: expected "F_U64" overlaps, found "F_U64" overlaps.\n", bucketSizes[i], num); + fprintf(stderr, "ERROR: expected " F_U64 " overlaps, found " F_U64 " overlaps.\n", bucketSizes[i], num); assert(num == bucketSizes[i]); delete bof; } if (ovlsLen != totOvl) - fprintf(stderr, "ERROR: read "F_U64" overlaps, expected "F_U64"\n", ovlsLen, totOvl); + fprintf(stderr, "ERROR: read " F_U64 " overlaps, expected " F_U64 "\n", ovlsLen, totOvl); assert(ovlsLen == totOvl); if (deleteIntermediateEarly) { diff --git a/src/stores/ovStoreStats.C b/src/stores/ovStoreStats.C index eccb44097..21acf25f5 100644 --- a/src/stores/ovStoreStats.C +++ b/src/stores/ovStoreStats.C @@ -589,20 +589,20 @@ main(int argc, char **argv) { fprintf(LOG, "category reads %% read length feature size or coverage analysis\n"); fprintf(LOG, "---------------- ------- ------- ---------------------- ------------------------ --------------------\n"); - fprintf(LOG, "middle-missing %7"F_U64P" %6.2f %10.2f +- %-8.2f %10.2f +- %-8.2f (bad trimming)\n", readHole->numberOfObjects(), (float)readHole->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readHole->mean(), readHole->stddev(), olapHole->mean(), olapHole->stddev()); - fprintf(LOG, "middle-hump %7"F_U64P" %6.2f %10.2f +- %-8.2f %10.2f +- %-8.2f (bad trimming)\n", readHump->numberOfObjects(), (float)readHump->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readHump->mean(), readHump->stddev(), olapHump->mean(), olapHump->stddev()); - fprintf(LOG, "no-5-prime %7"F_U64P" %6.2f %10.2f +- %-8.2f %10.2f +- %-8.2f (bad trimming)\n", readNo5->numberOfObjects(), (float)readNo5->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readNo5->mean(), readNo5->stddev(), olapNo5->mean(), olapNo5->stddev()); - fprintf(LOG, "no-3-prime %7"F_U64P" %6.2f %10.2f +- %-8.2f %10.2f +- %-8.2f (bad trimming)\n", readNo3->numberOfObjects(), (float)readNo3->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readNo3->mean(), readNo3->stddev(), olapNo3->mean(), olapNo3->stddev()); + fprintf(LOG, "middle-missing %7" F_U64P " %6.2f %10.2f +- %-8.2f %10.2f +- %-8.2f (bad trimming)\n", readHole->numberOfObjects(), (float)readHole->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readHole->mean(), readHole->stddev(), olapHole->mean(), olapHole->stddev()); + fprintf(LOG, "middle-hump %7" F_U64P " %6.2f %10.2f +- %-8.2f %10.2f +- %-8.2f (bad trimming)\n", readHump->numberOfObjects(), (float)readHump->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readHump->mean(), readHump->stddev(), olapHump->mean(), olapHump->stddev()); + fprintf(LOG, "no-5-prime %7" F_U64P " %6.2f %10.2f +- %-8.2f %10.2f +- %-8.2f (bad trimming)\n", readNo5->numberOfObjects(), (float)readNo5->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readNo5->mean(), readNo5->stddev(), olapNo5->mean(), olapNo5->stddev()); + fprintf(LOG, "no-3-prime %7" F_U64P " %6.2f %10.2f +- %-8.2f %10.2f +- %-8.2f (bad trimming)\n", readNo3->numberOfObjects(), (float)readNo3->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readNo3->mean(), readNo3->stddev(), olapNo3->mean(), olapNo3->stddev()); fprintf(LOG, "\n"); - fprintf(LOG, "low-coverage %7"F_U64P" %6.2f %10.2f +- %-8.2f %10.2f +- %-8.2f (easy to assemble, potential for lower quality consensus)\n", readLowCov->numberOfObjects(), (float)readLowCov->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readLowCov->mean(), readLowCov->stddev(), covrLowCov->mean(), covrLowCov->stddev()); - fprintf(LOG, "unique %7"F_U64P" %6.2f %10.2f +- %-8.2f %10.2f +- %-8.2f (easy to assemble, perfect, yay)\n", readUnique->numberOfObjects(), (float)readUnique->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readUnique->mean(), readUnique->stddev(), covrUnique->mean(), covrUnique->stddev()); - fprintf(LOG, "repeat-cont %7"F_U64P" %6.2f %10.2f +- %-8.2f %10.2f +- %-8.2f (potential for consensus errors, no impact on assembly)\n", readRepeatCont->numberOfObjects(), (float)readRepeatCont->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readRepeatCont->mean(), readRepeatCont->stddev(), covrRepeatCont->mean(), covrRepeatCont->stddev()); - fprintf(LOG, "repeat-dove %7"F_U64P" %6.2f %10.2f +- %-8.2f %10.2f +- %-8.2f (hard to assemble, likely won't assemble correctly or even at all)\n", readRepeatDove->numberOfObjects(), (float)readRepeatDove->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readRepeatDove->mean(), readRepeatDove->stddev(), covrRepeatDove->mean(), covrRepeatDove->stddev()); + fprintf(LOG, "low-coverage %7" F_U64P " %6.2f %10.2f +- %-8.2f %10.2f +- %-8.2f (easy to assemble, potential for lower quality consensus)\n", readLowCov->numberOfObjects(), (float)readLowCov->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readLowCov->mean(), readLowCov->stddev(), covrLowCov->mean(), covrLowCov->stddev()); + fprintf(LOG, "unique %7" F_U64P " %6.2f %10.2f +- %-8.2f %10.2f +- %-8.2f (easy to assemble, perfect, yay)\n", readUnique->numberOfObjects(), (float)readUnique->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readUnique->mean(), readUnique->stddev(), covrUnique->mean(), covrUnique->stddev()); + fprintf(LOG, "repeat-cont %7" F_U64P " %6.2f %10.2f +- %-8.2f %10.2f +- %-8.2f (potential for consensus errors, no impact on assembly)\n", readRepeatCont->numberOfObjects(), (float)readRepeatCont->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readRepeatCont->mean(), readRepeatCont->stddev(), covrRepeatCont->mean(), covrRepeatCont->stddev()); + fprintf(LOG, "repeat-dove %7" F_U64P " %6.2f %10.2f +- %-8.2f %10.2f +- %-8.2f (hard to assemble, likely won't assemble correctly or even at all)\n", readRepeatDove->numberOfObjects(), (float)readRepeatDove->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readRepeatDove->mean(), readRepeatDove->stddev(), covrRepeatDove->mean(), covrRepeatDove->stddev()); fprintf(LOG, "\n"); - fprintf(LOG, "span-repeat %7"F_U64P" %6.2f %10.2f +- %-8.2f %10.2f +- %-8.2f (read spans a large repeat, usually easy to assemble)\n", readSpanRepeat->numberOfObjects(), (float)readSpanRepeat->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readSpanRepeat->mean(), readSpanRepeat->stddev(), olapSpanRepeat->mean(), olapSpanRepeat->stddev()); - fprintf(LOG, "uniq-repeat-cont %7"F_U64P" %6.2f %10.2f +- %-8.2f (should be uniquely placed, low potential for consensus errors, no impact on assembly)\n", readUniqRepeatCont->numberOfObjects(), (float)readUniqRepeatCont->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readUniqRepeatCont->mean(), readUniqRepeatCont->stddev()); - fprintf(LOG, "uniq-repeat-dove %7"F_U64P" %6.2f %10.2f +- %-8.2f (will end contigs, potential to misassemble)\n", readUniqRepeatDove->numberOfObjects(), (float)readUniqRepeatDove->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readUniqRepeatDove->mean(), readUniqRepeatDove->stddev()); - fprintf(LOG, "uniq-anchor %7"F_U64P" %6.2f %10.2f +- %-8.2f %10.2f +- %-8.2f (repeat read, with unique section, probable bad read)\n", readUniqAnchor->numberOfObjects(), (float)readUniqAnchor->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readUniqAnchor->mean(), readUniqAnchor->stddev(), olapUniqAnchor->mean(), olapUniqAnchor->stddev()); + fprintf(LOG, "span-repeat %7" F_U64P " %6.2f %10.2f +- %-8.2f %10.2f +- %-8.2f (read spans a large repeat, usually easy to assemble)\n", readSpanRepeat->numberOfObjects(), (float)readSpanRepeat->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readSpanRepeat->mean(), readSpanRepeat->stddev(), olapSpanRepeat->mean(), olapSpanRepeat->stddev()); + fprintf(LOG, "uniq-repeat-cont %7" F_U64P " %6.2f %10.2f +- %-8.2f (should be uniquely placed, low potential for consensus errors, no impact on assembly)\n", readUniqRepeatCont->numberOfObjects(), (float)readUniqRepeatCont->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readUniqRepeatCont->mean(), readUniqRepeatCont->stddev()); + fprintf(LOG, "uniq-repeat-dove %7" F_U64P " %6.2f %10.2f +- %-8.2f (will end contigs, potential to misassemble)\n", readUniqRepeatDove->numberOfObjects(), (float)readUniqRepeatDove->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readUniqRepeatDove->mean(), readUniqRepeatDove->stddev()); + fprintf(LOG, "uniq-anchor %7" F_U64P " %6.2f %10.2f +- %-8.2f %10.2f +- %-8.2f (repeat read, with unique section, probable bad read)\n", readUniqAnchor->numberOfObjects(), (float)readUniqAnchor->numberOfObjects()/gkpStore->gkStore_getNumReads()*100, readUniqAnchor->mean(), readUniqAnchor->stddev(), olapUniqAnchor->mean(), olapUniqAnchor->stddev()); if (toFile == true) fclose(LOG); diff --git a/src/stores/tgStore.C b/src/stores/tgStore.C index 1de32bfe6..7180ea4fd 100644 --- a/src/stores/tgStore.C +++ b/src/stores/tgStore.C @@ -269,7 +269,7 @@ tgStore::writeTigToDisk(tgTig *tig, tgStoreEntry *te) { te->flushNeeded = 0; te->fileOffset = AS_UTL_ftell(FP); - //fprintf(stderr, "tgStore::writeTigToDisk()-- write tig "F_S32" in store version "F_U64" at file position "F_U64"\n", + //fprintf(stderr, "tgStore::writeTigToDisk()-- write tig " F_S32 " in store version " F_U64 " at file position " F_U64 "\n", // tig->_tigID, te->svID, te->fileOffset); tig->saveToStream(FP); @@ -409,7 +409,7 @@ tgStore::loadTig(uint32 tigID) { bool cantLoad = true; if (_tigLen <= tigID) - fprintf(stderr, "tgStore::loadTig()-- WARNING: invalid out-of-range tigID "F_S32", only "F_S32" ma in store; return NULL.\n", + fprintf(stderr, "tgStore::loadTig()-- WARNING: invalid out-of-range tigID " F_S32 ", only " F_S32 " ma in store; return NULL.\n", tigID, _tigLen); assert(tigID < _tigLen); @@ -684,7 +684,7 @@ tgStore::loadMASR(tgStoreEntry* &R, uint32& L, uint32& M, uint32 V) { // Check we're consistent. if (L < MASRtotalInFile) - fprintf(stderr, "tgStore::loadMASR()-- '%s' has more tigs ("F_U32") than expected ("F_U32").\n", + fprintf(stderr, "tgStore::loadMASR()-- '%s' has more tigs (" F_U32 ") than expected (" F_U32 ").\n", _name, MASRtotalInFile, L), exit(1); AS_UTL_safeRead(F, R, "MASR", sizeof(tgStoreEntry), masrLen); diff --git a/src/stores/tgStoreCompress.C b/src/stores/tgStoreCompress.C index 32fe4277d..4a47f9c16 100644 --- a/src/stores/tgStoreCompress.C +++ b/src/stores/tgStoreCompress.C @@ -51,7 +51,7 @@ operationCompress(char *tigName, int tigVers) { continue; if (tigStore->getVersion(ti) > tigVers) { - fprintf(stderr, "WARNING: Attempt to move future unitig "F_U32" from version "F_U32" to previous version %d.\n", + fprintf(stderr, "WARNING: Attempt to move future unitig " F_U32 " from version " F_U32 " to previous version %d.\n", ti, tigStore->getVersion(ti), tigVers); nErrors++; } else if (tigStore->getVersion(ti) < tigVers) { @@ -61,7 +61,7 @@ operationCompress(char *tigName, int tigVers) { if (nErrors > 0) { fprintf(stderr, "Store can't be compressed; probably trying to compress to something that isn't the latest version.\n"); - fprintf(stderr, " "F_U32" tigs failed; "F_U32" compressable\n", nErrors, nCompress); + fprintf(stderr, " " F_U32 " tigs failed; " F_U32 " compressable\n", nErrors, nCompress); delete tigStore; exit(1); } @@ -75,7 +75,7 @@ operationCompress(char *tigName, int tigVers) { } if (nCompress > 0) { - fprintf(stderr, "Compressing "F_U32" tigs into version %d\n", nCompress, tigVers); + fprintf(stderr, "Compressing " F_U32 " tigs into version %d\n", nCompress, tigVers); for (uint32 ti=0; tinumTigs(); ti++) { if ((ti % 1000000) == 0) @@ -102,7 +102,7 @@ operationCompress(char *tigName, int tigVers) { if (nCompress > 0) { for (uint32 version=1; versionpurgeVersion(version); } } diff --git a/src/stores/tgStoreCoverageStat.C b/src/stores/tgStoreCoverageStat.C index 9c4caa4fe..a32021b05 100644 --- a/src/stores/tgStoreCoverageStat.C +++ b/src/stores/tgStoreCoverageStat.C @@ -213,8 +213,8 @@ getGlobalArrivalRate(tgStore *tigStore, fprintf(outSTA, "BASED ON ALL UNITIGS:\n"); fprintf(outSTA, "sumRho: %.0f\n", sumRho); - fprintf(outSTA, "totalRandomFrags: "F_U64"\n", totalRandom); - fprintf(outSTA, "Supplied genome size "F_U64"\n", genomeSize); + fprintf(outSTA, "totalRandomFrags: " F_U64 "\n", totalRandom); + fprintf(outSTA, "Supplied genome size " F_U64 "\n", genomeSize); fprintf(outSTA, "Computed genome size: %.2f\n", totalRandom / globalRate); fprintf(outSTA, "Calculated Global Arrival rate: %f\n", globalRate); diff --git a/src/stores/tgStoreDump.C b/src/stores/tgStoreDump.C index a59b9ee55..b16e0d1f0 100644 --- a/src/stores/tgStoreDump.C +++ b/src/stores/tgStoreDump.C @@ -250,7 +250,7 @@ dumpStatus(gkStore *UNUSED(gkpStore), tgStore *tigStore) { void dumpTig(FILE *out, tgTig *tig, bool useGapped) { - fprintf(out, F_U32"\t"F_U32"\t%s\t%.2f\t%.2f\t%s\t%s\t%s\t"F_U32"\n", + fprintf(out, F_U32"\t" F_U32 "\t%s\t%.2f\t%.2f\t%s\t%s\t%s\t" F_U32 "\n", tig->tigID(), tig->length(useGapped), tig->coordinateType(useGapped), @@ -266,7 +266,7 @@ dumpTig(FILE *out, tgTig *tig, bool useGapped) { void dumpRead(FILE *out, tgTig *tig, tgPosition *read, bool useGapped) { - fprintf(out, F_U32"\t"F_U32"\t%s\t"F_U32"\t"F_U32"\n", + fprintf(out, F_U32"\t" F_U32 "\t%s\t" F_U32 "\t" F_U32 "\n", read->ident(), tig->tigID(), tig->coordinateType(useGapped), @@ -549,7 +549,7 @@ plotDepthHistogram(char *N, uint64 *cov, uint32 covMax) { fprintf(stderr, "Failed to open '%s' for writing: %s\n", N, strerror(errno)); for (uint32 ii=minii; ii<=maxii; ii++) - fprintf(F, F_U32"\t"F_U64"\n", ii, cov[ii]); + fprintf(F, F_U32"\t" F_U64 "\n", ii, cov[ii]); fclose(F); } @@ -1243,13 +1243,13 @@ main (int argc, char **argv) { filter.tigIDend = nTigs-1; if (nTigs <= filter.tigIDend) { - fprintf(stderr, "WARNING: adjusting tig ID range from "F_U32"-"F_U32" to "F_U32"-"F_U32" as there are only "F_U32" tigs in the store.\n", + fprintf(stderr, "WARNING: adjusting tig ID range from " F_U32 "-" F_U32 " to " F_U32 "-" F_U32 " as there are only " F_U32 " tigs in the store.\n", filter.tigIDbgn, filter.tigIDend, filter.tigIDbgn, nTigs-1, nTigs); filter.tigIDend = nTigs - 1; } if (filter.tigIDend < filter.tigIDbgn) { - fprintf(stderr, "WARNING: adjusting inverted tig ID range -t "F_U32"-"F_U32"\n", + fprintf(stderr, "WARNING: adjusting inverted tig ID range -t " F_U32 "-" F_U32 "\n", filter.tigIDbgn, filter.tigIDend); uint32 x = filter.tigIDend; filter.tigIDend = filter.tigIDbgn; @@ -1257,7 +1257,7 @@ main (int argc, char **argv) { } if (nTigs <= filter.tigIDbgn) - fprintf(stderr, "ERROR: only "F_U32" tigs in the store (IDs 0-"F_U32" inclusive); can't dump requested range -t "F_U32"-"F_U32"\n", + fprintf(stderr, "ERROR: only " F_U32 " tigs in the store (IDs 0-" F_U32 " inclusive); can't dump requested range -t " F_U32 "-" F_U32 "\n", nTigs, nTigs-1, filter.tigIDbgn, filter.tigIDend), exit(1); diff --git a/src/stores/tgStoreFilter.C b/src/stores/tgStoreFilter.C index 1d2fa61d5..3b67bf281 100644 --- a/src/stores/tgStoreFilter.C +++ b/src/stores/tgStoreFilter.C @@ -557,14 +557,14 @@ main(int argc, char **argv) { } fprintf(outSTA, "classification number of unitigs total length\n"); - fprintf(outSTA, " unique: %17"F_U32P" %14"F_U64P"\n", repeat_IsUnique.num, repeat_IsUnique.len); - fprintf(outSTA, " singleton: %17"F_U32P" %14"F_U64P"\n", repeat_IsSingleton.num, repeat_IsSingleton.len); - fprintf(outSTA, " repeat: %17"F_U32P" %14"F_U64P"\n", repeat_IsRepeat.num, repeat_IsRepeat.len); - fprintf(outSTA, " too few reads: %17"F_U32P" %14"F_U64P"\n", repeat_LowReads.num, repeat_LowReads.len); - fprintf(outSTA, " low cov stat: %17"F_U32P" %14"F_U64P"\n", repeat_LowCovStat.num, repeat_LowCovStat.len); - fprintf(outSTA, " too short: %17"F_U32P" %14"F_U64P"\n", repeat_Short.num, repeat_Short.len); - fprintf(outSTA, " spanning read: %17"F_U32P" %14"F_U64P"\n", repeat_SingleSpan.num, repeat_SingleSpan.len); - fprintf(outSTA, " low coverage: %17"F_U32P" %14"F_U64P"\n", repeat_LowCov.num, repeat_LowCov.len); + fprintf(outSTA, " unique: %17" F_U32P " %14" F_U64P "\n", repeat_IsUnique.num, repeat_IsUnique.len); + fprintf(outSTA, " singleton: %17" F_U32P " %14" F_U64P "\n", repeat_IsSingleton.num, repeat_IsSingleton.len); + fprintf(outSTA, " repeat: %17" F_U32P " %14" F_U64P "\n", repeat_IsRepeat.num, repeat_IsRepeat.len); + fprintf(outSTA, " too few reads: %17" F_U32P " %14" F_U64P "\n", repeat_LowReads.num, repeat_LowReads.len); + fprintf(outSTA, " low cov stat: %17" F_U32P " %14" F_U64P "\n", repeat_LowCovStat.num, repeat_LowCovStat.len); + fprintf(outSTA, " too short: %17" F_U32P " %14" F_U64P "\n", repeat_Short.num, repeat_Short.len); + fprintf(outSTA, " spanning read: %17" F_U32P " %14" F_U64P "\n", repeat_SingleSpan.num, repeat_SingleSpan.len); + fprintf(outSTA, " low coverage: %17" F_U32P " %14" F_U64P "\n", repeat_LowCov.num, repeat_LowCov.len); fclose(outLOG); fclose(outSTA); diff --git a/src/stores/tgTig.C b/src/stores/tgTig.C index 26545ac80..b84cdfcdb 100644 --- a/src/stores/tgTig.C +++ b/src/stores/tgTig.C @@ -454,7 +454,7 @@ tgTig::dumpLayout(FILE *F) { if (_gappedLen > 0) assert(_gappedLen == _layoutLen); - fprintf(F, "tig "F_U32"\n", _tigID); + fprintf(F, "tig " F_U32 "\n", _tigID); fprintf(F, "len %d\n", _layoutLen); // Adjust QV's to Sanger encoding @@ -485,7 +485,7 @@ tgTig::dumpLayout(FILE *F) { fprintf(F, "class %s\n", toString(_class)); fprintf(F, "suggestRepeat %c\n", _suggestRepeat ? 'T' : 'F'); fprintf(F, "suggestCircular %c\n", _suggestCircular ? 'T' : 'F'); - fprintf(F, "numChildren "F_U32"\n", _childrenLen); + fprintf(F, "numChildren " F_U32 "\n", _childrenLen); // And the reads. @@ -503,15 +503,15 @@ tgTig::dumpLayout(FILE *F) { if (imp->_isRead) - fprintf(F, "read %9"F_U32P" anchor %9"F_U32P" hang %7"F_S32P" %7"F_S32P" position %9"F_U32P" %9"F_U32P"%s%s\n", + fprintf(F, "read %9" F_U32P " anchor %9" F_U32P " hang %7" F_S32P " %7" F_S32P " position %9" F_U32P " %9" F_U32P "%s%s\n", imp->ident(), imp->anchor(), imp->aHang(), imp->bHang(), imp->bgn(), imp->end(), trimString, deltaString); if (imp->_isUnitig) - fprintf(F, "unitig %9"F_U32P" anchor %9"F_U32P" hang %7"F_S32P" %7"F_S32P" position %9"F_U32P" %9"F_U32P"%s%s\n", + fprintf(F, "unitig %9" F_U32P " anchor %9" F_U32P " hang %7" F_S32P " %7" F_S32P " position %9" F_U32P " %9" F_U32P "%s%s\n", imp->ident(), imp->anchor(), imp->aHang(), imp->bHang(), imp->bgn(), imp->end(), trimString, deltaString); if (imp->_isContig) - fprintf(F, "contig %9"F_U32P" anchor %9"F_U32P" hang %7"F_S32P" %7"F_S32P" position %9"F_U32P" %9"F_U32P"%s%s\n", + fprintf(F, "contig %9" F_U32P " anchor %9" F_U32P " hang %7" F_S32P " %7" F_S32P " position %9" F_U32P " %9" F_U32P "%s%s\n", imp->ident(), imp->anchor(), imp->aHang(), imp->bHang(), imp->bgn(), imp->end(), trimString, deltaString); } @@ -578,7 +578,7 @@ tgTig::loadLayout(FILE *F) { else if (strcmp(W[1], "contig") == 0) _class = tgTig_contig; else - fprintf(stderr, "tgTig::loadLayout()-- '%s' line "F_U64" invalid: '%s'\n", W[0], LINEnum, LINE), exit(1); + fprintf(stderr, "tgTig::loadLayout()-- '%s' line " F_U64 " invalid: '%s'\n", W[0], LINEnum, LINE), exit(1); } else if (strcmp(W[0], "suggestRepeat") == 0) { _suggestRepeat = strtouint32(W[1]); @@ -595,7 +595,7 @@ tgTig::loadLayout(FILE *F) { (strcmp(W[0], "contig") == 0)) { if (W.numWords() < 10) - fprintf(stderr, "tgTig::loadLayout()-- '%s' line "F_U64" invalid: '%s'\n", W[0], LINEnum, LINE), exit(1); + fprintf(stderr, "tgTig::loadLayout()-- '%s' line " F_U64 " invalid: '%s'\n", W[0], LINEnum, LINE), exit(1); if (nChildren >= _childrenLen) { resizeArray(_children, _childrenLen, _childrenMax, _childrenLen + 1, resizeArray_copyData); @@ -664,7 +664,7 @@ void tgTig::dumpFASTA(FILE *F, bool useGapped) { AS_UTL_writeFastA(F, bases(useGapped), length(useGapped), 100, - ">tig%08u len="F_U32" reads="F_U32" covStat=%.2f gappedBases=%s class=%s suggestRepeat=%s suggestCircular=%s\n", + ">tig%08u len=" F_U32 " reads=" F_U32 " covStat=%.2f gappedBases=%s class=%s suggestRepeat=%s suggestCircular=%s\n", tigID(), length(useGapped), numberOfChildren(), @@ -681,7 +681,7 @@ tgTig::dumpFASTQ(FILE *F, bool useGapped) { AS_UTL_writeFastQ(F, bases(useGapped), length(useGapped), quals(useGapped), length(useGapped), - "@tig%08u len="F_U32" reads="F_U32" covStat=%.2f gappedBases=%s class=%s suggestRepeat=%s suggestCircular=%s\n", + "@tig%08u len=" F_U32 " reads=" F_U32 " covStat=%.2f gappedBases=%s class=%s suggestRepeat=%s suggestCircular=%s\n", tigID(), length(useGapped), numberOfChildren(), diff --git a/src/stores/tgTigSizeAnalysis.C b/src/stores/tgTigSizeAnalysis.C index 2a9741414..60733c01f 100644 --- a/src/stores/tgTigSizeAnalysis.C +++ b/src/stores/tgTigSizeAnalysis.C @@ -73,6 +73,7 @@ tgTigSizeAnalysis::evaluateTig(tgTig *tig, bool useGapped) { case tgTig_unassembled: lenUnassembled.push_back(length); break; case tgTig_bubble: lenBubble.push_back(length); break; case tgTig_contig: lenContig.push_back(length); break; + default: break; } } @@ -112,7 +113,7 @@ tgTigSizeAnalysis::printSummary(FILE *out, char *description, vector &da sum += data[i]; while (siz * nnn / 100 < sum) { - fprintf(out, "%s ng%-3"F_U64P" %10"F_U32P" bp lg%-3"F_U64P" %6"F_U64P" sum %10"F_U64P" bp\n", + fprintf(out, "%s ng%-3" F_U64P " %10" F_U32P " bp lg%-3" F_U64P " %6" F_U64P " sum %10" F_U64P " bp\n", description, nnn, data[i], nnn, i+1, @@ -122,9 +123,9 @@ tgTigSizeAnalysis::printSummary(FILE *out, char *description, vector &da } } - fprintf(out, "%s sum %10"F_U64P" (genomeSize "F_U64")\n", description, tot, genomeSize); - fprintf(out, "%s num %10"F_U64P"\n", description, cnt); - fprintf(out, "%s ave %10"F_U64P"\n", description, tot / cnt); + fprintf(out, "%s sum %10" F_U64P " (genomeSize " F_U64 ")\n", description, tot, genomeSize); + fprintf(out, "%s num %10" F_U64P "\n", description, cnt); + fprintf(out, "%s ave %10" F_U64P "\n", description, tot / cnt); } diff --git a/src/utgcns/libNDalign/NDalign.C b/src/utgcns/libNDalign/NDalign.C index 215308eea..267f9182d 100644 --- a/src/utgcns/libNDalign/NDalign.C +++ b/src/utgcns/libNDalign/NDalign.C @@ -473,7 +473,7 @@ NDalign::findHits(void) { if ((apos - bpos < _minDiag) || (apos - bpos > _maxDiag)) - fprintf(stderr, "NDalign::findHits()-- kmer "F_X64" apos - bpos = %d _minDiag = %d _maxDiag = %d\n", + fprintf(stderr, "NDalign::findHits()-- kmer " F_X64 " apos - bpos = %d _minDiag = %d _maxDiag = %d\n", kmer, apos-bpos, _minDiag, _maxDiag); assert(apos - bpos >= _minDiag); // ...these too. assert(apos - bpos <= _maxDiag); diff --git a/src/utgcns/libcns/unitigConsensus.C b/src/utgcns/libcns/unitigConsensus.C index dfcdd669d..cc1888cc5 100644 --- a/src/utgcns/libcns/unitigConsensus.C +++ b/src/utgcns/libcns/unitigConsensus.C @@ -287,17 +287,17 @@ unitigConsensus::generatePBDAG(tgTig *tig_, uint32 end = utgpos[i].max(); if (start > utg.seq.length()) { - fprintf(stderr, "WARNING: reset start from "F_U32" to "F_U64"\n", start, utg.seq.length()-1); + fprintf(stderr, "WARNING: reset start from " F_U32 " to " F_U64 "\n", start, utg.seq.length()-1); start = utg.seq.length() - 1; } if (end - start > readLen) { - fprintf(stderr, "WARNING: reset end from "F_U32" to "F_U32"\n", end, start+readLen); + fprintf(stderr, "WARNING: reset end from " F_U32 " to " F_U32 "\n", end, start+readLen); end = start + readLen; } if (end > utg.seq.length()) { - fprintf(stderr, "WARNING: truncate end from "F_U32" to "F_U64"\n", end, utg.seq.length()-1); + fprintf(stderr, "WARNING: truncate end from " F_U32 " to " F_U64 "\n", end, utg.seq.length()-1); end = utg.seq.length() - 1; } diff --git a/src/utgcns/stashContains.C b/src/utgcns/stashContains.C index 8d0fd6c4b..96280fa1c 100644 --- a/src/utgcns/stashContains.C +++ b/src/utgcns/stashContains.C @@ -238,7 +238,7 @@ unstashContains(tgTig *tig, } if (idmap.empty() == false) - fprintf(stderr, "Failed to unstash the contained reads. Still have "F_SIZE_T" reads unplaced.\n", + fprintf(stderr, "Failed to unstash the contained reads. Still have " F_SIZE_T " reads unplaced.\n", idmap.size()); assert(idmap.empty() == true); diff --git a/src/utgcns/stashContains.H b/src/utgcns/stashContains.H index 8ae97be30..d40a11b10 100644 --- a/src/utgcns/stashContains.H +++ b/src/utgcns/stashContains.H @@ -76,14 +76,14 @@ public: }; void reportDetected(FILE *out, uint32 id) { - fprintf(out, " unitig %d detected "F_S32" contains (%.2fx, %.2f%%) "F_S32" dovetail (%.2fx, %.2f%%)\n", + fprintf(out, " unitig %d detected " F_S32 " contains (%.2fx, %.2f%%) " F_S32 " dovetail (%.2fx, %.2f%%)\n", id, numContains, covContain, percContain, numDovetails, covDovetail, percDovetail); }; void reportRemoved(FILE *out, uint32 id) { - fprintf(out, " unitig %d removing "F_S32" (%.2fx) contained reads; processing only "F_S32" contained (%.2fx) and "F_S32" dovetail (%.2fx) reads\n", + fprintf(out, " unitig %d removing " F_S32 " (%.2fx) contained reads; processing only " F_S32 " contained (%.2fx) and " F_S32 " dovetail (%.2fx) reads\n", id, numContainsRemoved, covContainsRemoved, numContainsSaved, covContainsSaved, diff --git a/src/utgcns/utgcns.C b/src/utgcns/utgcns.C index b9b6809e6..18fbf01da 100644 --- a/src/utgcns/utgcns.C +++ b/src/utgcns/utgcns.C @@ -349,10 +349,10 @@ main (int argc, char **argv) { // Report some sizes. - fprintf(stderr, "sizeof(abBead) "F_SIZE_T"\n", sizeof(abBead)); - fprintf(stderr, "sizeof(abColumn) "F_SIZE_T"\n", sizeof(abColumn)); - fprintf(stderr, "sizeof(abAbacus) "F_SIZE_T"\n", sizeof(abAbacus)); - fprintf(stderr, "sizeof(abSequence) "F_SIZE_T"\n", sizeof(abSequence)); + fprintf(stderr, "sizeof(abBead) " F_SIZE_T "\n", sizeof(abBead)); + fprintf(stderr, "sizeof(abColumn) " F_SIZE_T "\n", sizeof(abColumn)); + fprintf(stderr, "sizeof(abAbacus) " F_SIZE_T "\n", sizeof(abAbacus)); + fprintf(stderr, "sizeof(abSequence) " F_SIZE_T "\n", sizeof(abSequence)); // Decide on what to compute. Either all unitigs, or a single unitig, or a special case test. @@ -372,12 +372,12 @@ main (int argc, char **argv) { e = utgEnd; } - fprintf(stderr, "-- Computing unitig consensus for b="F_U32" to e="F_U32" with errorRate %0.4f (max %0.4f) and minimum overlap "F_U32"\n", + fprintf(stderr, "-- Computing unitig consensus for b=" F_U32 " to e=" F_U32 " with errorRate %0.4f (max %0.4f) and minimum overlap " F_U32 "\n", b, e, errorRate, errorRateMax, minOverlap); } else { - fprintf(stderr, "-- Computing unitig consensus with errorRate %0.4f (max %0.4f) and minimum overlap "F_U32"\n", + fprintf(stderr, "-- Computing unitig consensus with errorRate %0.4f (max %0.4f) and minimum overlap " F_U32 "\n", errorRate, errorRateMax, minOverlap); }