bwa aln produces inconsistent behavior when recording the mapped status of multiply mapping reads. In most cases, such reads are flagged as mapped with a mapq of 0. However, we have discovered some cases where these reads are flagged as unmapped.
prymer currently relies on the unmapped flag to identify reads with a hit count of zero. This has been yielding errors when attempting to parse reads in the latter category. This information can instead be obtained directly from the HN tag.
Closes #68
bwa alnproduces inconsistent behavior when recording the mapped status of multiply mapping reads. In most cases, such reads are flagged as mapped with a mapq of 0. However, we have discovered some cases where these reads are flagged as unmapped.prymercurrently relies on the unmapped flag to identify reads with a hit count of zero. This has been yielding errors when attempting to parse reads in the latter category. This information can instead be obtained directly from theHNtag.