Without thorough testing to show otherwise, it must be assumed that bin3C relies on BWA MEM to build the BAM file, while also relying that BWA MEM was run with the option -5 or perhaps even more specifically -5SP. This expectation is in addition to sorting by query name.
We already check for sorting order, but do not try to check for BWA MEM options.
bin3C should check immediately that the @PG record contains bwa mem and -5 option.
Without thorough testing to show otherwise, it must be assumed that bin3C relies on BWA MEM to build the BAM file, while also relying that BWA MEM was run with the option
-5or perhaps even more specifically-5SP. This expectation is in addition to sorting by query name.We already check for sorting order, but do not try to check for BWA MEM options.
bin3C should check immediately that the @PG record contains
bwa memand-5option.Failure should be reported as a warning.