Open jenniferliddle opened 7 years ago
For what it's worth, the modification of FLAG dates back to this commit: https://github.com/samtools/samtools/commit/140d53dfdfe32bfa3ae4b24f1f33d071f366054f and the notion of it being something to warn about samtools/samtools@a8c861864486f4c30dc664e3378ffd6e021b6364.
Both of these are 0.1.5, prior to the htslib split. However just because it's been doing this for years doesn't necessarily make it valid! My own view is it's an error in the implementation.
When htslib reads a BAM record, if there is no cigar string the 'unmapped' flag is set and a warning message sent to stderr. This is contrary to the SAM specification, which says that
It's not clear to me if changing this behaviour would cause more problems than it solves.