diff --git a/src/bamToBed/bamToBed.cpp b/src/bamToBed/bamToBed.cpp index 432a0f6398a2bced6e55b328a7051c706dbd20cb..c89441a02a6c387bb5075ae028ee06a319a7db8f 100644 --- a/src/bamToBed/bamToBed.cpp +++ b/src/bamToBed/bamToBed.cpp @@ -479,13 +479,26 @@ void PrintBed(const BamAlignment &bam, const RefVector &refs, unsigned int i; for (i = 0; i < bedBlocks.size(); ++i) { BED curr = bedBlocks[i]; - printf("%s\t%d\t%d\t\%s\t%d\t%s\n", - chrom.c_str(), - curr.start, - curr.end, - name.c_str(), - bam.MapQuality, - strand.c_str()); + + if (bamTag == "") { + printf("%s\t%d\t%d\t\%s\t%d\t%s\n", + chrom.c_str(), + curr.start, + curr.end, + name.c_str(), + bam.MapQuality, + strand.c_str()); + } + else { + cout << chrom << "\t" + << bam.Position << "\t" + << curr.start << "\t" + << curr.end << "\t" + << name << "\t" + << PrintTag(bam, bamTag) << "\t" + << strand + << endl; + } } } }