minor fixes utgcns, properly handle skip bases in layouts

marbl · Jul 24, 2024 · f405dd3 · f405dd3
1 parent f1cfd2a
commit f405dd3
Show file tree

Hide file tree

Showing 3 changed files with 6 additions and 7 deletions.
diff --git a/src/stores/tgTig.H b/src/stores/tgTig.H
@@ -116,7 +116,7 @@ public:
   uint32               deltaLength(void)     { return(_deltaLen);    };
 
   //  Set everything.  This is to be used by unitigger.
-  void                 set(uint32 id, uint32 anchor, int32 ahang, int32 bhang, int32  bgn, int32  end) {
+  void                 set(uint32 id, uint32 anchor, int32 ahang, int32 bhang, int32  bgn, int32  end, uint32 askip = 0, uint32 bskip = 0) {
 
     _objID         = id;
 
@@ -130,8 +130,8 @@ public:
     _ahang         = ahang;
     _bhang         = bhang;
 
-    _askip         = 0;
-    _bskip         = 0;
+    _askip         = askip;
+    _bskip         = bskip;
 
     _min           = std::min(bgn, end);
     _max           = std::max(bgn, end);

diff --git a/src/utgcns/layoutToPackage.C b/src/utgcns/layoutToPackage.C
@@ -118,7 +118,7 @@ loadVerkkoLayouts(sqCache              *reads,
       if (readMap)
         fprintf(readMap, "%10u  %10u  %s\n", id, tig->tigID(), W[0]);
 
-      ch->set(id, pa, askp, bskp, bgn, end);
+      ch->set(id, pa, 0, 0, bgn, end, askp, bskp);
       ch->skipConsensus(ignore);
 
       if ((W.numWords() < 3) || (W.numWords() > 5))

diff --git a/src/utgcns/unitigConsensus.C b/src/utgcns/unitigConsensus.C
@@ -695,7 +695,7 @@ alignEdLib(dagAlignment      &aln,
   int32  tigend = std::min((int32)tiglen, (int32)floor(utgpos.max() + padding));
 
   if (verbose)
-    fprintf(stderr, "alignEdLib()-- align read %7u padding %d maxpad %d eRate %.4f at %9d-%-9d\n", utgpos.ident(), padding, maxpad, bandErrRate, tigbgn, tigend);
+    fprintf(stderr, "alignEdLib()-- align read %7u padding %7u maxpad %7u eRate %.4f at %9d-%-9d\n", utgpos.ident(), padding, maxpad, bandErrRate, tigbgn, tigend);
 
   if (tigend < tigbgn) {
     fprintf(stderr, "alignEdLib()-- WARNING: tigbgn %d > tigend %d - tiglen %d utgpos %d-%d padding %d\n",
@@ -1182,8 +1182,7 @@ unitigConsensus::findCoordinates(char algorithm_, u32toRead  &reads_) {
 
     //  Decide on where to align this read and the expected quality.
 
-    int32  maxpad   = (_tig->getChild(ii)->isLowQuality() == true) ? MAX_PADDING : MAX_PADDING;  //  Pad low-quality reads by at most
-    int32  padding  = std::min(maxpad, (int32)ceil(readlen * 0.05));                             //  2.5Kbp, high-quality by only 250bp.
+    int32  padding  = std::min(MAX_PADDING, (int32)ceil(readlen * 0.05));
 
     int32  bandpad[9]  = {  1 * padding,  5 * padding, MAX_PADDING_MULT * padding,
                             1 * padding,  5 * padding, MAX_PADDING_MULT * padding,