Update meryl/ and utility/: 'types.H' changes and 64-mer lookups.

wolongac · Nov 30, 2020 · aa43bb5 · aa43bb5
1 parent 76b1263
commit aa43bb5
Show file tree

Hide file tree

Showing 6 changed files with 7 additions and 6 deletions.
diff --git a/src/correction/falconConsensus-alignTag.C b/src/correction/falconConsensus-alignTag.C
@@ -92,8 +92,8 @@ getAlignTags(char       *Qalign,   int32 Qbgn,  int32 Qlen, int32 UNUSED(Qid),
     assert(j >= 0);
     assert(j <  Tlen);
 
-    if ((jj   >= uint16MAX) ||
-        (p_jj >= uint16MAX))
+    if ((jj   >= uint16max) ||
+        (p_jj >= uint16max))
       continue;
 
     tags->setTag(j, p_j, jj, p_jj, Qalign[k], p_q_base);

diff --git a/src/correction/falconConsensus.C b/src/correction/falconConsensus.C
@@ -100,7 +100,7 @@ falconConsensus::getConsensus(uint32         tagsLen,                //  Number
       // Assume t_pos was set on earlier iteration.
       // (Otherwise, use its initial value, which might be an error. ~cd)
 
-      assert(tag->delta < uint16MAX);
+      assert(tag->delta < uint16max);
 
       msa[t_pos]->increaseDeltaGroup(tag->delta);
 

diff --git a/src/main.mk b/src/main.mk
@@ -31,6 +31,7 @@ SOURCES      := utility/src/utility/runtime.C \
                 utility/src/utility/kmers.C \
                 \
                 utility/src/utility/bits.C \
+                utility/src/utility/bits-wordArray.C \
                 \
                 utility/src/utility/hexDump.C \
                 utility/src/utility/md5.C \

diff --git a/src/meryl b/src/meryl
diff --git a/src/stores/ovStoreConfig.C b/src/stores/ovStoreConfig.C
@@ -321,7 +321,7 @@ main(int argc, char **argv) {
     } else if (strcmp(argv[arg], "-M") == 0) {
       double lo=0.0, hi=0.0;
 
-      decodeRange(argv[++arg], lo, hi);
+      decodeRange<double>(argv[++arg], lo, hi);
 
       minMemory = (uint64)ceil(lo * 1024.0 * 1024.0 * 1024.0);
       maxMemory = (uint64)ceil(hi * 1024.0 * 1024.0 * 1024.0);

diff --git a/src/utility b/src/utility
+147 −0		scripts/buildRelease.sh
+1 −1		scripts/version_update.pl
+13 −30		src/Makefile
+2 −0		src/main.mk
+382 −0		src/meryl-analyze/meryl-analyze.C
+8 −0		src/meryl-analyze/meryl-analyze.mk
+23 −34		src/meryl-check/meryl-check.C
+2 −2		src/meryl-import/meryl-import.C
+276 −100		src/meryl-lookup/meryl-lookup.C
+9 −9		src/meryl/meryl.C
+4 −9		src/meryl/merylCommandBuilder.C
+19 −19		src/meryl/merylCountArray.C
+37 −16		src/meryl/merylCountArray.H
+3 −0		src/meryl/merylInput.H
+46 −89		src/meryl/merylOp-count.C
+1 −1		src/meryl/merylOp-countSimple.C
+109 −75		src/meryl/merylOp-countThreads.C
+1 −1		src/meryl/merylOp-histogram.C
+1 −1		src/tests/merylCountArrayTest.C
+1 −1		src/utility
+3 −1		src/main.mk
+26 −2		src/tests/bitsTest.C
+135 −0		src/tests/typesTest.C
+8 −0		src/tests/typesTest.mk
+114 −0		src/utility/bits-wordArray.C
+128 −0		src/utility/bits-wordArray.H
+54 −0		src/utility/bits.C
+75 −225		src/utility/bits.H
+2 −2		src/utility/files-compressed.C
+28 −25		src/utility/kmers-exact.C
+155 −139		src/utility/kmers-lookup.H
+12 −9		src/utility/kmers-tiny.H
+7 −4		src/utility/kmers-writer.C
+1 −1		src/utility/kmers-writer.H
+5 −5		src/utility/mt19937ar.C
+33 −13		src/utility/sequence.C
+13 −2		src/utility/sequence.H
+2 −2		src/utility/speedCounter.H
+81 −147		src/utility/strings.C
+80 −113		src/utility/strings.H
+60 −63		src/utility/system.C
+475 −41		src/utility/types.C
+247 −83		src/utility/types.H