Fix crash with tiny alignments and fix incorrect check for circulariz…

…ation
TankMermaid · Nov 13, 2020 · 4b8448f · 4b8448f
1 parent ab08d0c
commit 4b8448f
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Showing 2 changed files with 7 additions and 5 deletions.
diff --git a/src/bogart/AS_BAT_FindCircular.C b/src/bogart/AS_BAT_FindCircular.C
@@ -236,14 +236,15 @@ findCircularContigs(TigVector &tigs,
     ufNode          *fRead = tig->firstBackboneRead();
     ufNode          *lRead = tig->lastBackboneRead();
 
+    bool        invert = (fRead->position.isForward() != lRead->position.isForward());
     uint32      circularLength = 0;
     uint32      ovlLen = 0;
     BAToverlap *ovl    = OC->getOverlaps(lRead->ident, ovlLen);
 
     for (uint32 oo=0; oo<ovlLen; oo++) {
       if ((ovl[oo].b_iid == fRead->ident) &&
-          (((lRead->position.isForward() ==  true) && (ovl[oo].AEndIs3prime() ==  true)) ||
-           ((lRead->position.isForward() == false) && (ovl[oo].AEndIs5prime() ==  true))))
+          (((lRead->position.isForward() ==  true) && (ovl[oo].AEndIs3prime() ==  true) && (ovl[oo].flipped == invert))  ||
+           ((lRead->position.isForward() == false) && (ovl[oo].AEndIs5prime() ==  true) && (ovl[oo].flipped == invert))))
 
         //  Circular!
         circularLength = RI->overlapLength(lRead->ident, fRead->ident, ovl[oo].a_hang, ovl[oo].b_hang);

diff --git a/src/utgcns/unitigConsensus.C b/src/utgcns/unitigConsensus.C
@@ -1352,9 +1352,10 @@ unitigConsensus::trimCircular(void) {
     align.alignDovetail(bases, length, length-trylen, length,           //  A:  the end of the tig
                         bases, length, 0,             trylen, false);   //  B:  the start of the tig
 
-    if ((align.errorRate() < 0.05) &&         //  "Found" if the error rate is reasonable, and
-        (align.bgnA() > length - trylen) &&   //  A has unaligned stuff at the start, and
-        (align.endB() < trylen))              //  B has unaligned stuff at the end.
+    if ((align.errorRate() < 0.05) &&                //  "Found" if the error rate is reasonable, and
+        (align.alignmentLength() >= _minOverlap) &&  //  and length is reasonable
+        (align.bgnA() > length - trylen) &&          //  A has unaligned stuff at the start, and
+        (align.endB() < trylen))                     //  B has unaligned stuff at the end.
       found = true;
 
     if ((found == false) && (showPlacement()))