Actually enforce minReadLength when computing corrected reads.

wolongac · Sep 18, 2020 · f978ef6 · f978ef6
1 parent 268b8c3
commit f978ef6
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Showing 2 changed files with 9 additions and 14 deletions.
diff --git a/src/correction/falconConsensus.H b/src/correction/falconConsensus.H
@@ -165,12 +165,10 @@ public:
 class falconConsensus {
 public:
   falconConsensus(uint32               minOutputCoverage_,
-                  uint32               minOutputLength_,
                   double               minOlapIdentity_,
                   uint32               minOlapLength_,
                   bool                 restrictToOverlap_ = true) {
     minOutputCoverage   = minOutputCoverage_;
-    minOutputLength     = minOutputLength_;
     minOlapIdentity     = minOlapIdentity_;
     minOlapLength       = minOlapLength_;
     restrictToOverlap   = restrictToOverlap_;
@@ -229,7 +227,6 @@ public:
 
 private:
   uint32               minOutputCoverage;
-  uint32               minOutputLength;
 
   double               minOlapIdentity;
   uint32               minOlapLength;

diff --git a/src/correction/falconsense.C b/src/correction/falconsense.C
@@ -458,7 +458,7 @@ main(int argc, char **argv) {
   //  partitioning, but that would be wrong, because partitioning uses these objects to determine
   //  the base amount of memory needed.
 
-  falconConsensus           *fc = new falconConsensus(minOutputCoverage, minOutputLength, minOlapIdentity, minOlapLength, restrictToOverlap);
+  falconConsensus           *fc = new falconConsensus(minOutputCoverage, minOlapIdentity, minOlapLength, restrictToOverlap);
   map<uint32, sqRead *>      reads;
 
   if (memoryLimit == 0) {
@@ -485,11 +485,10 @@ main(int argc, char **argv) {
                               trimToAlign,
                               minOlapLength);
 
-      if (cnsFile)
-        layout->saveToStream(cnsFile);
-
-      if (seqFile)
-        layout->dumpFASTQ(seqFile);
+      if (layout->length() >= minOutputLength) {
+        if (cnsFile)   layout->saveToStream(cnsFile);
+        if (seqFile)   layout->dumpFASTQ(seqFile);
+      }
 
       delete layout;
       layout = new tgTig();    //  Next loop needs an existing empty layout.
@@ -701,11 +700,10 @@ main(int argc, char **argv) {
         fc = NULL;
 #endif
 
-        if (cnsFile)
-          layout->saveToStream(cnsFile);
-
-        if (seqFile)
-          layout->dumpFASTQ(seqFile);
+        if (layout->length() >= minOutputLength) {
+          if (cnsFile)   layout->saveToStream(cnsFile);
+          if (seqFile)   layout->dumpFASTQ(seqFile);
+        }
 
         corStore->unloadTig(layout->tigID());
       }