modified: src/AlignmentProfile.cpp

modified: src/ReadAlignment.cpp modified: src/VariantCalling.cpp
hsinnan75 · Oct 7, 2019 · fb076cf · fb076cf
1 parent df12fab
commit fb076cf
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Showing 3 changed files with 5 additions and 2 deletions.
diff --git a/src/AlignmentProfile.cpp b/src/AlignmentProfile.cpp
@@ -75,7 +75,7 @@ void UpdateProfile(ReadItem_t* read, vector<AlnCan_t>& AlnCanVec)
 		//if (bSomatic && iter->PairedAlnCanIdx == -1) continue;
 
 		if (iter->orientation) gPos = iter->FragPairVec.begin()->gPos;
-		else gPos = TwoGenomeSize - 1 - iter->FragPairVec.begin()->gPos;
+		else gPos = TwoGenomeSize - (iter->FragPairVec.begin()->gPos + iter->FragPairVec.begin()->gLen);
 		if (MappingRecordArr[gPos].readCount < iMaxDuplicate) MappingRecordArr[gPos].readCount++;
 		else continue;
 

diff --git a/src/ReadAlignment.cpp b/src/ReadAlignment.cpp
@@ -427,6 +427,9 @@ bool ProduceReadAlignment(ReadItem_t& read)
 	//		{
 	//			//Display alignments
 	//			//pthread_mutex_lock(&Lock);
+	//			if (iter->orientation) printf("StartPos=%lld\n", iter->FragPairVec.begin()->gPos);
+	//			else printf("StartPos=%lld\n", TwoGenomeSize - (iter->FragPairVec.begin()->gPos + iter->FragPairVec.begin()->gLen));
+
 	//			printf("read: %s, score=%d (%d/%d) len=%d, PairedIdx=%d\n\n", read.header, iter->score, read.AlnSummary.score, read.AlnSummary.sub_score, read.rlen, iter->PairedAlnCanIdx);
 	//			ShowSimplePairInfo(iter->FragPairVec);
 	//			//pthread_mutex_unlock(&Lock);

diff --git a/src/VariantCalling.cpp b/src/VariantCalling.cpp
@@ -566,7 +566,7 @@ void *IdentifyVariants(void *arg)
 
 	for (; gPos < end; gPos++)
 	{
-		if ((ref_base = nst_nt4_table[(unsigned short)RefSequence[gPos]]) < 4)
+		if ((ref_base = nst_nt4_table[(unsigned short)RefSequence[gPos]]) != 4)
 		{
 			bNormal = true; cov = GetProfileColumnSize(MappingRecordArr[gPos]);
 			//if (bSomatic && (MappingRecordArr[gPos].multi_hit > (int)(cov*0.05))) continue;