Fix calls to gkpStore and switch to -S instead of -G flags

HealthVivo · Apr 18, 2018 · 885d634 · 885d634
1 parent 01d1823
commit 885d634
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Showing 2 changed files with 6 additions and 7 deletions.
diff --git a/src/pipelines/canu/Unitig.pm b/src/pipelines/canu/Unitig.pm
@@ -222,8 +222,8 @@ sub unitig ($) {
         print F "  mv ./$asm.utgStore ../$asm.utgStore\n";
         print F "fi\n";
     } elsif (getGlobal("unitigger") eq "wtdbg") {
-        print F "\$bin/gatekeeperDumpFASTQ \\\n";
-        print F "  -G ../$asm.gkpStore \\\n";
+        print F "\$bin/sqStoreDumpFASTQ \\\n";
+        print F "  -S ../$asm.seqStore \\\n";
         print F "  -nolibname \\\n";
         print F "  -noreadname \\\n";
         print F "  -fasta \\\n";
@@ -251,7 +251,7 @@ sub unitig ($) {
         print F "fi\n";
         print F "\n";
         print F "\n";
-        print F " \$bin/wtdbgConvert -o ./$asm -G ../$asm.gkpStore $asm.ctg.lay \\\n";
+        print F " \$bin/wtdbgConvert -o ./$asm -S ../$asm.seqStore $asm.ctg.lay \\\n";
         print F "  && \\\n";
         print F "  cp -r ./$asm.ctgStore ../$asm.utgStore \\\n";
         print F "  && \\\n";

diff --git a/src/wtdbg/wtdbgConvert.C b/src/wtdbg/wtdbgConvert.C
@@ -38,7 +38,7 @@
 using namespace std;
 
 double MIN_READ_FRACTION = 0.5;
-double MAX_READ_STRETCH  = 1.3;
+double MAX_READ_STRETCH  = 1.2;
 
 void save_tig(sqStore *seqStore, tgStore *tigStore, tgTig *tig,
               map<uint32, map<uint32, int32> > &readToStart,
@@ -127,7 +127,7 @@ main(int argc, char **argv) {
     if        (strcmp(argv[arg], "-o") == 0) {
       outName = argv[++arg];
 
-    } else if (strcmp(argv[arg], "-G") == 0) {
+    } else if (strcmp(argv[arg], "-S") == 0) {
       seqName = argv[++arg];
 
     } else if (AS_UTL_fileExists(argv[arg])) {
@@ -150,7 +150,7 @@ main(int argc, char **argv) {
     fprintf(stderr, "\n");
 
     if (seqName == NULL)
-      fprintf(stderr, "ERROR:  no seqStore (-G) supplied\n");
+      fprintf(stderr, "ERROR:  no seqStore (-S) supplied\n");
     if (files.size() == 0)
       fprintf(stderr, "ERROR:  no overlap files supplied\n");
 
@@ -232,7 +232,6 @@ main(int argc, char **argv) {
              end            = int(offset) + W(4);
           }
          if (readToStart.find(rid) == readToStart.end() || readToStart[rid].find(index) == readToStart[rid].end()) {
-             if (bgn < 0) continue; 
              readToStart[rid][index] = max(0, bgn);
              readToEnd[rid][index] = end;
              readPieces[rid][index] = 1;