Remove some old filters - small test results are the same as in the previous commit.
@@ -27,17 +27,6 @@ int chimericAlignScore (ChimericSegment & seg1, ChimericSegment & seg2)
bool ReadAlign::chimericDetectionMult() {
bool chimRecord=false;
-
- //////////////////// chimeras
- //stich windows => chimeras
- //stich only the best window with one of the lower score ones for now - do not stich 2 lower score windows
- //stitch only one window on each end of the read
-
- if (nTr>P.pCh.mainSegmentMultNmax && nTr!=2)
- {//multimapping main segment, nTr==2 is a special case to be checked later
- return chimRecord;
- };
-
vector <ChimericAlign> chimAligns;
int chimScoreBest=0;
@@ -110,15 +99,6 @@ bool ReadAlign::chimericDetectionMult() {
};//cycle over window1 aligns
};//cycle over window1
- if (nTr>P.pCh.mainSegmentMultNmax)
- {//check main segment for multi-aligns
- //this is nTr==2 - a special case: chimeras are allowed only if the 2nd chimeric segment is the next best alignment
- if ( &chimAligns[0].seg2.align!=trMult[0] && &chimAligns[0].seg2.align!=trMult[1] )
- {
- return chimRecord;
- };
- };
-
if (chimScoreBest==0)
return chimRecord;
