fix the crash when outputing overlapped file

sfchen · sfchen · commit 1517e86e13ea · 2025-06-17T18:23:56.000+08:00
#616
diff --git a/src/peprocessor.cpp b/src/peprocessor.cpp
@@ -461,7 +461,7 @@ bool PairEndProcessor::processPairEnd(ReadPack* leftPack, ReadPack* rightPack, T
         if(r1 != NULL && r2!=NULL && mOverlappedWriter) {
             OverlapResult ov = OverlapAnalysis::analyze(r1, r2, mOptions->overlapDiffLimit, mOptions->overlapRequire, 0);
             if(ov.overlapped) {
-                Read* overlappedRead = new Read(r1->mName, new string(r1->mSeq->substr(max(0,ov.offset)), ov.overlap_len), r1->mStrand, new string(r1->mQuality->substr(max(0,ov.offset)), ov.overlap_len));
+                Read* overlappedRead = new Read(new string(*r1->mName), new string(r1->mSeq->substr(max(0,ov.offset)), ov.overlap_len), new string(*r1->mStrand), new string(r1->mQuality->substr(max(0,ov.offset)), ov.overlap_len));
                 overlappedRead->appendToString(overlappedOut);
                 recycleToPool1(tid, overlappedRead);
             }

Original file line number	Diff line number	Diff line change
`@@ -461,7 +461,7 @@ bool PairEndProcessor::processPairEnd(ReadPack* leftPack, ReadPack* rightPack, T`
`461`	`461`	`if(r1 != NULL && r2!=NULL && mOverlappedWriter) {`
`462`	`462`	`OverlapResult ov = OverlapAnalysis::analyze(r1, r2, mOptions->overlapDiffLimit, mOptions->overlapRequire, 0);`
`463`	`463`	`if(ov.overlapped) {`
`464`		`- Read* overlappedRead = new Read(r1->mName, new string(r1->mSeq->substr(max(0,ov.offset)), ov.overlap_len), r1->mStrand, new string(r1->mQuality->substr(max(0,ov.offset)), ov.overlap_len));`
	`464`	`+ Read* overlappedRead = new Read(new string(r1->mName), new string(r1->mSeq->substr(max(0,ov.offset)), ov.overlap_len), new string(r1->mStrand), new string(r1->mQuality->substr(max(0,ov.offset)), ov.overlap_len));`
`465`	`465`	`overlappedRead->appendToString(overlappedOut);`
`466`	`466`	`recycleToPool1(tid, overlappedRead);`
`467`	`467`	`}`