Remove qs and qq tags after the clipped sequence has been reinserted

dozy · dozy · commit fd1706085fb8 · 2014-03-21T14:47:48.000Z
diff --git a/src/biobambam/ClipReinsert.cpp b/src/biobambam/ClipReinsert.cpp
@@ -27,6 +27,10 @@ bool clipReinsert(
 	std::stack < libmaus::bambam::cigar_operation > & hardstack
 )
 {
+        libmaus::bambam::BamAuxFilterVector auxfilter;
+        auxfilter.set("qs");
+        auxfilter.set("qq");
+
 	uint64_t const numaux = algn.enumerateAuxTags(auxtags);
 	for ( uint64_t i = 0; i < numaux; ++i )
 		bafv.set(auxtags[i].first,auxtags[i].second);
@@ -86,6 +90,8 @@ bool clipReinsert(
 			algn.replaceSequence(read + qs, qual + qq);
 		else
 			algn.replaceSequence( libmaus::fastx::reverseComplementUnmapped(qs) + read, std::string(qq.rbegin(),qq.rend()) + qual);
+
+		algn.filterOutAux(auxfilter);
 	}
 
 	for ( uint64_t i = 0; i < numaux; ++i )

Original file line number	Diff line number	Diff line change
`@@ -27,6 +27,10 @@ bool clipReinsert(`
`27`	`27`	`std::stack < libmaus::bambam::cigar_operation > & hardstack`
`28`	`28`	`)`
`29`	`29`	`{`
	`30`	`+ libmaus::bambam::BamAuxFilterVector auxfilter;`
	`31`	`+ auxfilter.set("qs");`
	`32`	`+ auxfilter.set("qq");`
	`33`	`+`
`30`	`34`	`uint64_t const numaux = algn.enumerateAuxTags(auxtags);`
`31`	`35`	`for ( uint64_t i = 0; i < numaux; ++i )`
`32`	`36`	`bafv.set(auxtags[i].first,auxtags[i].second);`
`@@ -86,6 +90,8 @@ bool clipReinsert(`
`86`	`90`	`algn.replaceSequence(read + qs, qual + qq);`
`87`	`91`	`else`
`88`	`92`	`algn.replaceSequence( libmaus::fastx::reverseComplementUnmapped(qs) + read, std::string(qq.rbegin(),qq.rend()) + qual);`
	`93`	`+`
	`94`	`+ algn.filterOutAux(auxfilter);`
`89`	`95`	`}`
`90`	`96`
`91`	`97`	`for ( uint64_t i = 0; i < numaux; ++i )`