Merge pull request #601 from genommm/master

sfchen · web-flow · commit 25d4600c77a1 · 2025-04-16T07:31:32.000+08:00
Pull for issue #600 Update peprocessor.cpp: fix duplicate pointer deletion when --overlapped is used.
diff --git a/src/peprocessor.cpp b/src/peprocessor.cpp
@@ -461,7 +461,10 @@ bool PairEndProcessor::processPairEnd(ReadPack* leftPack, ReadPack* rightPack, T
             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));
                 overlappedRead->appendToString(overlappedOut);
-                recycleToPool1(tid, overlappedRead);
+                overlappedRead->mName = nullptr;
+                overlappedRead->mStrand = nullptr;
+                delete overlappedRead;
+                //recycleToPool1(tid, overlappedRead);
             }
         }
 

Original file line number	Diff line number	Diff line change
`@@ -461,7 +461,10 @@ bool PairEndProcessor::processPairEnd(ReadPack* leftPack, ReadPack* rightPack, T`
`461`	`461`	`if(ov.overlapped) {`
`462`	`462`	`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));`
`463`	`463`	`overlappedRead->appendToString(overlappedOut);`
`464`		`- recycleToPool1(tid, overlappedRead);`
	`464`	`+ overlappedRead->mName = nullptr;`
	`465`	`+ overlappedRead->mStrand = nullptr;`
	`466`	`+ delete overlappedRead;`
	`467`	`+ //recycleToPool1(tid, overlappedRead);`
`465`	`468`	`}`
`466`	`469`	`}`
`467`	`470`