htslib_wrapper: in the general mapping format changed the parsing criteria for the genomic region to ignore whether or not the mapping is primary. If the parsing can be done, it should. The client can decide whether or not to consider if it is primary

Author: andrewdavidsmith

htslib_wrapper.cpp

@@ -417,7 +417,7 @@ SAMReader::get_SAMRecord_general(const string &str, SAMRecord &samr) {
   samr.seg_len = seg_len;
   samr.mr.r.set_name(name);
 
-  if (samr.is_primary && samr.is_mapped) {
+  if (samr.is_mapped) {
     samr.mr.r.set_chrom(chrom);
     samr.mr.r.set_start(start - 1);
     samr.mr.r.set_score(0);