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Fix Segmentation Fault Under Certain Conditions #1

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Fix Segmentation Fault Under Certain Conditions #1

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c418578
Fix Segmentation Fault Under Certain Conditions
evolvedmicrobe Dec 5, 2018
927e0c7
Fix assumption that difference was only 1
Dec 5, 2018
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16 changes: 9 additions & 7 deletions source/ReadAlign_maxMappableLength2strands.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -58,12 +58,7 @@ uint ReadAlign::maxMappableLength2strands(uint pieceStartIn, uint pieceLengthIn,
maxL=0;
Nrep = maxMappableLength(Read1, pieceStart, pieceLength, G, SA, iSA1 & P->SAiMarkNmask, iSA2, dirR, maxL, indStartEnd, P);
#else
if (Lind < P->genomeSAindexNbases && (iSA1 & P->SAiMarkNmaskC)==0 ) {//no need for SA search
indStartEnd[0]=iSA1;
indStartEnd[1]=iSA2;
Nrep=indStartEnd[1]-indStartEnd[0]+1;
maxL=Lind;
} else if (iSA1==iSA2) {//unique align already, just find maxL
if (iSA1==iSA2) {//unique align already, just find maxL
if ((iSA1 & P->SAiMarkNmaskC)!=0) {
ostringstream errOut;
errOut << "BUG: in ReadAlign::maxMappableLength2strands";
Expand All @@ -75,7 +70,14 @@ uint ReadAlign::maxMappableLength2strands(uint pieceStartIn, uint pieceLengthIn,
maxL=compareSeqToGenome(Read1,pieceStart, pieceLength, Lind, G, SA, iSA1, dirR, comparRes, P);
} else {//SA search, pieceLength>maxL
if ( (iSA1 & P->SAiMarkNmaskC)==0 ) {//no N in the prefix
maxL=Lind;
// iSA2 can now point to a suffix with multiple "N" bases, eg. this sort order
// ACTGAAAA <- iSA1
// ACTGNNNN <- iSA2
// ACTTACTG <- next prefix
// As a result, we can only assume the match length is as good up to
// the length that iSA2 hits, and need to compare everything past that length in the binary search
bool cres;
maxL=compareSeqToGenome(Read1,pieceStart, pieceLength, 0, G, SA, iSA2, dirR, cres, P);
} else {
maxL=0;
};
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