Dear biobambam2 team,
bamsort fails if the @PG header is malformed. In my case, the @PG line is missing the word "ID:" after processing the BAM file with another tool. While strictly speaking, the header IS malformatted, I would rather suggest to issue a simple warning message at that point, instead of terminating the program.
Technically, it's not a big deal to edit the header and re-header the BAM files. Practically, in existing pipelines (based on SAMtools), I will have to check for this error message and correct the file before re-running the pipeline, although the @PG line is dispensable for sorting. :)
Dear biobambam2 team, bamsort fails if the @PG header is malformed. In my case, the @PG line is missing the word "ID:" after processing the BAM file with another tool. While strictly speaking, the header IS malformatted, I would rather suggest to issue a simple warning message at that point, instead of terminating the program. Technically, it's not a big deal to edit the header and re-header the BAM files. Practically, in existing pipelines (based on SAMtools), I will have to check for this error message and correct the file before re-running the pipeline, although the @PG line is dispensable for sorting. :)
Thank you! Best Sergej