Remove support for 'gapped' consensus sequence.

arun-sub · Jul 15, 2019 · 92f8c95 · 92f8c95
1 parent 48b24d3
commit 92f8c95
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Showing 13 changed files with 227 additions and 422 deletions.
diff --git a/src/correction/falconsense.C b/src/correction/falconsense.C
@@ -216,17 +216,18 @@ generateFalconConsensus(falconConsensus           *fc,
   layout->_sourceBgn   = (end == 0) ? (0) : (fd->pos[bgn]);            //  Space based (probably).
   layout->_sourceEnd   = (end == 0) ? (0) : (fd->pos[end - 1] + 1);    //  Space based.
 
-  resizeArrayPair(layout->_gappedBases, layout->_gappedQuals, layout->_gappedLen, layout->_gappedMax, end - bgn + 1, resizeArray_doNothing);
+  resizeArrayPair(layout->_bases, layout->_quals, layout->_basesLen, layout->_basesMax, end - bgn + 1, resizeArray_doNothing);
 
   for (uint32 ii=bgn; ii<end; ii++) {
-    layout->_gappedBases[ii-bgn] = fd->seq[ii];
-    layout->_gappedQuals[ii-bgn] = fd->eqv[ii];
+    layout->_bases[ii-bgn] = fd->seq[ii];
+    layout->_quals[ii-bgn] = fd->eqv[ii];
   }
 
-  layout->_gappedLen = end - bgn;
+  layout->_layoutLen = end - bgn;
+  layout->_basesLen  = end - bgn;
 
-  layout->_gappedBases[layout->_gappedLen] = 0;
-  layout->_gappedQuals[layout->_gappedLen] = 0;
+  layout->_bases[layout->_basesLen] = 0;
+  layout->_quals[layout->_basesLen] = 0;
 
   //  One could dump bases and quals here, if so desired.
 
@@ -507,7 +508,7 @@ main(int argc, char **argv) {
         layout->saveToStream(cnsFile);
 
       if (seqFile)
-        layout->dumpFASTQ(seqFile, false);
+        layout->dumpFASTQ(seqFile);
 
       delete layout;
       layout = new tgTig();    //  Next loop needs an existing empty layout.
@@ -721,7 +722,7 @@ main(int argc, char **argv) {
           layout->saveToStream(cnsFile);
 
         if (seqFile)
-          layout->dumpFASTQ(seqFile, false);
+          layout->dumpFASTQ(seqFile);
 
         corStore->unloadTig(layout->tigID());
       }

diff --git a/src/gfa/alignGFA.C b/src/gfa/alignGFA.C
@@ -51,10 +51,10 @@ public:
   };
 
   void  set(tgTig *tig) {
-    len = tig->length(false);
+    len = tig->length();
     seq = new char [len + 1];
 
-    memcpy(seq, tig->bases(false), len);
+    memcpy(seq, tig->bases(), len);
 
     seq[len] = 0;
   };

diff --git a/src/stores/tgStore.C b/src/stores/tgStore.C
@@ -276,8 +276,8 @@ tgStore::insertTig(tgTig *tig, bool keepInCache) {
 
   //  Check that the components do not exceed the bound.
   //
-  if (tig->_gappedLen > 0) {
-    uint32  len = tig->_gappedLen;
+  if (tig->_basesLen > 0) {
+    uint32  len = tig->_basesLen;
     uint32  swp = 0;
     uint32  neg = 0;
     uint32  pos = 0;