Replace AS_UTL_fileExists() with pathExists(), fileExists() and direc…

…toryExists().

src/bogart/AS_BAT_OverlapCache.C

@@ -970,7 +970,7 @@ OverlapCache::load(void) {
   size_t   numRead;
 
   snprintf(name, FILENAME_MAX, "%s.ovlCache", _prefix);
-  if (AS_UTL_fileExists(name, false, false) == false)
+  if (fileExists(name) == false)
     return(false);
 
   writeStatus("OverlapCache()-- Loading graph from '%s'.\n", name);

src/bogart/addReadsToUnitigs.C

@@ -146,7 +146,7 @@ main(int argc, char **argv) {
         fprintf(stderr, "invalid tigStore version (-t store version) '-t %s %s'.\n", argv[arg-1], argv[arg]), exit(1);
 
     } else if (strcmp(argv[arg], "-m") == 0) {
-      while ((argv[arg+1] != NULL) && (AS_UTL_fileExists(argv[arg+1], false, false) == true))
+      while ((argv[arg+1] != NULL) && (fileExists(argv[arg+1]) == true))
         alignMapNames.push_back(argv[++arg]);
 
     } else if (strcmp(argv[arg], "-lookup") == 0) {

src/erateEstimate/erateEstimate.C

@@ -671,7 +671,7 @@ main(int argc, char **argv) {
   ESToverlap       *overlaps     = NULL;
   memoryMappedFile *overlapsMMF  = NULL;
 
-  if (AS_UTL_fileExists(ovlCacheName, false, false)) {
+  if (fileExists(ovlCacheName)) {
     fprintf(stderr, "  cache '%s' detected, load averted\n", ovlCacheName);
 
     overlapsMMF = new memoryMappedFile(ovlCacheName);

src/merTrim/merTrim.C

@@ -285,7 +285,7 @@ public:
     char  cacheName[FILENAME_MAX];
     snprintf(cacheName, FILENAME_MAX, "%s.merTrimDB", merCountsFile);
 
-    if (AS_UTL_fileExists(cacheName, false, false)) {
+    if (fileExists(cacheName)) {
       fprintf(stderr, "loading genome mer database from cache '%s'.\n", cacheName);
       genomicDB = new existDB(cacheName);
 

src/meryl-san/libkmer/existDB.C

@@ -76,7 +76,7 @@ existDB::existDB(char const    *filename,
   //  meryl database.
 
 
-  if (AS_UTL_fileExists(filename))
+  if (fileExists(filename))
     createFromFastA(filename, merSize, flags);
   else
     createFromMeryl(filename, merSize, lo, hi, flags);

src/meryl-san/libleaff/fastaFile.C

@@ -353,7 +353,7 @@ void
 fastaFile::loadIndex(char *indexname) {
   struct stat  fastastat;
 
-  if (AS_UTL_fileExists(indexname) == false)
+  if (fileExists(indexname) == false)
     return;
 
   errno = 0;

src/meryl-san/libleaff/fastqFile.C

@@ -350,7 +350,7 @@ void
 fastqFile::loadIndex(char *indexname) {
   struct stat  fastqstat;
 
-  if (AS_UTL_fileExists(indexname) == false)
+  if (fileExists(indexname) == false)
     return;
 
   errno = 0;

src/meryl-san/libleaff/sqStoreFile.C

@@ -63,9 +63,9 @@ sqStoreFile::openFile(const char *name) {
   sprintf(infoName, "%s/info",  name);
   sprintf(readName, "%s/reads", name);
 
-  if ((AS_UTL_fileExists(name, true) == false) ||
-      (AS_UTL_fileExists(infoName) == false) ||
-      (AS_UTL_fileExists(readName) == false))
+  if ((directoryExists(name) == false) ||
+      (fileExists(infoName)  == false) ||
+      (fileExists(readName)  == false))
     return(0L);
 
   //  Yup, probably a sqStore.  If it isn't, the sqStore() constructor blows up.

src/meryl-san/libmeryl-san.C

@@ -59,9 +59,9 @@ merylStreamReader::merylStreamReader(const char *fn_, uint32 ms_) {
   //  bitPackedFile will create a file if it doesn't exist, so we need to fail ahead
   //  of time.
 
-  bool idxexist = AS_UTL_fileExists(idxname);
-  bool datexist = AS_UTL_fileExists(datname);
-  bool posexist = AS_UTL_fileExists(posname);
+  bool idxexist = fileExists(idxname);
+  bool datexist = fileExists(datname);
+  bool posexist = fileExists(posname);
 
   if ((idxexist == false) ||
       (datexist == false)) {

src/meryl-san/maskMers.C

@@ -95,7 +95,7 @@ public:
     strncpy(_maskMersName, _merylName, FILENAME_MAX-1);
     strcat(_maskMersName, ".maskMers");
 
-    if (AS_UTL_fileExists(_maskMersName))
+    if (fileExists(_maskMersName))
       loadMasking(onlySeqIID_);
     else
       buildMasking();

src/meryl-san/meryl-build.C

@@ -354,7 +354,7 @@ runSegment(merylArgs *args, uint64 segment) {
 
   snprintf(filename, FILENAME_MAX, "%s.batch" F_U64 ".mcdat", args->outputFile, segment);
 
-  if (AS_UTL_fileExists(filename)) {
+  if (fileExists(filename)) {
     if (args->beVerbose)
       fprintf(stderr, "Found result for batch " F_U64 " in %s.\n", segment, filename);
     return;
@@ -690,10 +690,10 @@ build(merylArgs *args) {
 
   sprintf(N, "%s.existenceTest", args->outputFile);
 
-  if (AS_UTL_fileExists(args->outputFile, true) == true)
+  if (directoryExists(args->outputFile) == true)
     fprintf(stderr, "ERROR: output prefix -o cannot be a directory.\n"), exit(1);
 
-  if (AS_UTL_fileExists(N) == false) {
+  if (fileExists(N) == false) {
     errno = 0;
     FILE *F = fopen(N, "w");
     if (errno)

src/meryl-san/meryl-san.C

@@ -594,8 +594,8 @@ main(int argc, char **argv) {
 
     else if (arg == outputArg)                 writer = new merylStreamWriter(opt, merSize, 0, merSize/2, false);
 
-    else if (AS_UTL_fileExists(mcidx) &&
-             AS_UTL_fileExists(mcdat))         reader = new merylStreamReader(opt);
+    else if (fileExists(mcidx) &&
+             fileExists(mcdat))                reader = new merylStreamReader(opt);
 
     else {
       char *s = new char [1024];

src/meryl-san/positionDB.C

@@ -240,7 +240,7 @@ main(int argc, char **argv) {
 
   //  Exit quickly if the output file exists.
   //
-  if (AS_UTL_fileExists(outputFile)) {
+  if (fileExists(outputFile)) {
     fprintf(stderr, "Output file '%s' exists already!\n", outputFile);
     exit(0);
   }

src/meryl-san/simple-dump.C

@@ -82,7 +82,7 @@ main(int argc, char **argv) {
 
   //  Load existence mers from the saved existDB, or create a new existDB and maybe save to disk.
 
-  if ((existFile) && (AS_UTL_fileExists(existFile))) {
+  if ((existFile) && (fileExists(existFile))) {
     E = new existDB(existFile);
   }
 

src/meryl-san/utility/bitPackedFile.C

@@ -70,7 +70,7 @@ bitPackedFile::bitPackedFile(char const *name, uint64 offset, bool forceTruncate
     if (errno)
       fprintf(stderr, "bitPackedFile::bitPackedFile()-- failed to open and truncate '%s': %s\n",
               _name, strerror(errno)), exit(1);
-  } else if (AS_UTL_fileExists(_name)) {
+  } else if (fileExists(_name)) {
     errno = 0;
     _file = open(_name,
                  O_RDONLY | O_LARGEFILE,

src/meryl/meryl.C

@@ -253,7 +253,7 @@ main(int argc, char **argv) {
       writer = new kmerCountFileWriter(inoutName);        //  output writer.
 
     else if ((arg == printArg) &&                         //  This this _should_ have been an output name,
-             (AS_UTL_fileExists(inoutName, true))) {      //  but is instead a directory; user is asking for
+             (directoryExists(inoutName))) {              //  but is instead a directory; user is asking for
       printer = stdout;                                   //  the database in the directory to be printed.
       reader  = new kmerCountFileReader(inoutName);
     }
@@ -263,12 +263,12 @@ main(int argc, char **argv) {
 
     else if ((opStack.size() > 0) &&                      //  If a command exists,
              (opStack.top()->isCounting()  == false) &&   //  and it isn't for counting,
-             (AS_UTL_fileExists(indexName) == true))      //  and the meryl index file exists,
+             (fileExists(indexName) == true))             //  and the meryl index file exists,
       reader = new kmerCountFileReader(inoutName);        //  add a kmerCountFile as input to the current command.
 
     else if ((opStack.size() > 0) &&                      //  If a command exists,
              (opStack.top()->isCounting()  == true) &&    //  and it IS for counting,
-             (AS_UTL_fileExists(inoutName)  == true))     //  and the file exists,
+             (fileExists(inoutName)  == true))            //  and the file exists,
       sequence = new dnaSeqFile(inoutName);               //  add a sequence file as input to the current command.
 
     else {

src/mhap/mhapConvert.C

@@ -57,7 +57,7 @@ main(int argc, char **argv) {
     } else if (strcmp(argv[arg], "-S") == 0) {
       seqName = argv[++arg];
 
-    } else if (AS_UTL_fileExists(argv[arg])) {
+    } else if (fileExists(argv[arg])) {
       files.push_back(argv[arg]);
 
     } else {

src/minimap/mmapConvert.C

@@ -63,7 +63,7 @@ main(int argc, char **argv) {
     } else if (strcmp(argv[arg], "-len") == 0) {
       minOverlapLength = atoi(argv[++arg]);
 
-    } else if (AS_UTL_fileExists(argv[arg])) {
+    } else if (fileExists(argv[arg])) {
       files.push_back(argv[arg]);
 
     } else {

src/overlapBasedTrimming/clearRangeFile.H

@@ -47,7 +47,7 @@ public:
 
     strncpy(_fileName, fileName, FILENAME_MAX-1);
 
-    if (AS_UTL_fileExists(_fileName) == false) {
+    if (fileExists(_fileName) == false) {
       _modified = true;   //  Always gets written, regardless of changes
 
       _lastID   = seq->sqStore_getNumReads();

src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C

@@ -116,7 +116,7 @@ main(int argc, char **argv) {
 
     sprintf(N, "%s/prefixEditDistance-matchLimit-%04d.bin", D, evalue);
 
-    if (AS_UTL_fileExists(N)) {
+    if (fileExists(N)) {
       fprintf(stderr, "eValue %04d -- eRate %6.4f -- %7.4f%% error -- %8d values -- thread %2d - LOAD\n",
               evalue, erate, erate * 100.0, MAX_ERRORS, omp_get_thread_num());
 

src/overlapInCore/overlapConvert.C

@@ -60,7 +60,7 @@ main(int argc, char **argv) {
     } else if (strcmp(argv[arg], "-unaligned") == 0) {
       dt = ovOverlapAsUnaligned;
 
-    } else if (AS_UTL_fileExists(argv[arg])) {
+    } else if (fileExists(argv[arg])) {
       files.push_back(argv[arg]);
 
     } else {

src/overlapInCore/overlapImport.C

@@ -141,7 +141,7 @@ main(int argc, char **argv) {
     }
 
     else if ((strcmp(argv[arg], "-") == 0) ||
-               (AS_UTL_fileExists(argv[arg]))) {
+             (fileExists(argv[arg]))) {
       files.push_back(argv[arg]);
     }
 

src/overlapInCore/overlapPair.C

@@ -770,7 +770,7 @@ main(int argc, char **argv) {
   ovFile           *ovlFile  = NULL;
   ovFile           *outFile  = NULL;
 
-  if (AS_UTL_fileExists(ovlName, true)) {
+  if (directoryExists(ovlName)) {
     fprintf(stderr, "Reading overlaps from store '%s' and writing to '%s'\n",
             ovlName, outName);
     ovlStore = new ovStore(ovlName, seqStore);

src/sequence/sequence.C

@@ -1454,7 +1454,7 @@ main(int argc, char **argv) {
 
     //  INPUTS
 
-    else if (AS_UTL_fileExists(argv[arg]) == true) {
+    else if (fileExists(argv[arg]) == true) {
       inputs.push_back(argv[arg]);
     }
 

src/stores/loadCorrectedReads.C

@@ -64,7 +64,7 @@ main (int argc, char **argv) {
     } else if (strcmp(argv[arg], "-qv") == 0) {
       loadQVs = true;
 
-    } else if (AS_UTL_fileExists(argv[arg])) {
+    } else if (fileExists(argv[arg])) {
       corInputs.push_back(argv[arg]);
 
     } else {

src/stores/loadErates.C

@@ -96,7 +96,7 @@ ovStore::addEvalues(vector<char *> &fileList) {
     _evalues    = NULL;
   }
 
-  if (AS_UTL_fileExists(evalueName) == true) {
+  if (fileExists(evalueName) == true) {
     fprintf(stderr, "WARNING:\n");
     fprintf(stderr, "WARNING: existing evalue file will be overwritten!\n");
     fprintf(stderr, "WARNING:\n");
@@ -197,7 +197,7 @@ main(int argc, char **argv) {
       AS_UTL_loadFileList(argv[++arg], fileList);
 
     } else if (((argv[arg][0] == '-') && (argv[arg][1] == 0)) ||
-               (AS_UTL_fileExists(argv[arg]))) {
+               (fileExists(argv[arg]))) {
       fileList.push_back(argv[arg]);        //  Assume it's an input file
 
     } else {

src/stores/ovStore.C

@@ -104,7 +104,7 @@ ovStore::ovStore(const char *path, sqStore *seq) {
 
   snprintf(name, FILENAME_MAX, "%s/evalues", _storePath);
 
-  if (AS_UTL_fileExists(name)) {
+  if (fileExists(name)) {
     _evaluesMap  = new memoryMappedFile(name, memoryMappedFile_readOnly);
     _evalues     = (uint16 *)_evaluesMap->get(0);
   }

src/stores/ovStoreBucketizer.C

@@ -173,7 +173,7 @@ main(int argc, char **argv) {
   snprintf(sliceSName, FILENAME_MAX, "%s/create%04u/sliceSizes", ovlName, bucketNum);  //  sliceSizes name before rename.
   snprintf(bucketName, FILENAME_MAX, "%s/bucket%04u",            ovlName, bucketNum);
 
-  if (AS_UTL_fileExists(createName, true, false) == true) {
+  if (directoryExists(createName) == true) {
     if (forceOverwrite) {
       fprintf(stderr, "Overwriting incomplete result from presumed crashed job in directory '%s'.\n", createName);
     } else {
@@ -182,7 +182,7 @@ main(int argc, char **argv) {
     }
   }
 
-  if (AS_UTL_fileExists(bucketName, false, false) == true) {
+  if (directoryExists(bucketName) == true) {
     fprintf(stderr, "Job finished; file '%s' exists.\n", sliceSName);
     exit(0);
   }

src/stores/ovStoreConfig.C

@@ -347,7 +347,7 @@ main(int argc, char **argv) {
       writeSlices = strtouint32(argv[++arg]);
 
     } else if (((argv[arg][0] == '-') && (argv[arg][1] == 0)) ||
-               (AS_UTL_fileExists(argv[arg]))) {
+               (fileExists(argv[arg]))) {
       //  Assume it's an input file
       fileList.push_back(argv[arg]);
 

src/stores/ovStoreFile.H

@@ -165,7 +165,7 @@ public:
     //  should have sent in a NULL prefix!) used when constructing the store.
     //  Return with no counts allocated and trust that the user doesn't try to access them.
 
-    if (AS_UTL_fileExists(name) == false)
+    if (fileExists(name) == false)
       return;
 
     //  Otherwise, counts exist, and we load them.

src/stores/ovStoreHistogram.C

@@ -103,8 +103,8 @@ ovStoreHistogram::ovStoreHistogram(const char *path) {
 
   createDataName(name, path);
 
-  if (AS_UTL_fileExists(name, false, false) == false)    //  If no data, nothing to
-    return;                                              //  load, so leave it empty.
+  if (fileExists(name) == false)    //  If no data, nothing to
+    return;                         //  load, so leave it empty.
 
   //  Load!
 
@@ -154,7 +154,7 @@ ovStoreHistogram::ovStoreHistogram(const char *path) {
 char *
 ovStoreHistogram::createDataName(char *name, const char *prefix) {
 
-  if (AS_UTL_fileExists(prefix, true, false)) {              //  If name is a directory,
+  if (directoryExists(prefix)) {                             //  If name is a directory,
     snprintf(name, FILENAME_MAX, "%s/statistics", prefix);   //  return a file in the directory.
   }
 

src/stores/ovStoreSorter.C

@@ -61,7 +61,7 @@ checkSentinel(const char *ovlName, uint32 sliceNum, ovStoreConfig *config) {
 
   snprintf(N, FILENAME_MAX, "%s/%04u.started", ovlName, sliceNum);
 
-  if (AS_UTL_fileExists(N, true, false) == true) {
+  if (fileExists(N) == true) {
     fprintf(stderr, "Job (appears to be) in progress; sentinel file '%s' exists.\n", N);
     exit(1);
   }

src/stores/ovStoreWriter.C

@@ -227,7 +227,7 @@ ovStoreSliceWriter::loadBucketSizes(uint64 *bucketSizes) {
 
     //  If no file, there are no overlaps, so nothing to load.
 
-    if (AS_UTL_fileExists(name, false, false) == false)
+    if (fileExists(name) == false)
       continue;
 
     //  Load the slice sizes, and save the number of overlaps in this slice.
@@ -257,7 +257,7 @@ ovStoreSliceWriter::loadOverlapsFromBucket(uint32 bucket, uint64 expectedLen, ov
 
   snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bucket, _sliceNum);
 
-  if (AS_UTL_fileExists(name, false, false) == false)
+  if (fileExists(name) == false)
     fprintf(stderr, "ERROR: " F_U64 " overlaps claim to exist in bucket '%s', but file not found.\n",
             expectedLen, name), exit(1);
 
@@ -503,8 +503,8 @@ ovStoreSliceWriter::checkSortingIsComplete(void) {
     snprintf(nameF, FILENAME_MAX, "%s/%04u.info",  _storePath, i);
     snprintf(nameI, FILENAME_MAX, "%s/%04u.index", _storePath, i);
 
-    bool existF = AS_UTL_fileExists(nameF, false, false);
-    bool existI = AS_UTL_fileExists(nameI, false, false);
+    bool existF = fileExists(nameF);
+    bool existI = fileExists(nameI);
 
     if (existF && existI)
       continue;
@@ -542,7 +542,7 @@ ovStoreSliceWriter::removeAllIntermediateFiles(void) {
       ovFile::createDataName(name, _storePath, ss, pp);
       ovStoreHistogram::createDataName(nomo, name);
 
-      if (AS_UTL_fileExists(nomo) == false)
+      if (fileExists(nomo) == false)
         break;
 
       AS_UTL_unlink(nomo);