apply patch from issue
@@ -189,8 +189,8 @@ void ProcessBedPE(BedFilePE *bedpe, GenomeFile *genome, int mapQual, bool uncom
if (bedpe->bedType >= 10) {
ConvertBedPEToBam(bedpeEntry, bamEntry1, bamEntry2, chromToId, mapQual, lineNum);
- writer->SaveAlignment(bamEntry1);
- writer->SaveAlignment(bamEntry2);
+ writer->SaveAlignment(bamEntry1, true);
+ writer->SaveAlignment(bamEntry2, true);
}
else {
