Sort BAM with incorrect bin

[tylo42]

I have a BAM where the bin was set incorrectly. When running sambamba sort the following error message is printed and sorting is aborted:

sambamba-sort: Bin in read with name 'XXX' is set incorrectly (5784 instead of expected 90)

This corresponds to https://github.com/biod/BioD/blob/master/bio/bam/bai/indexing.d#L251.

On the same BAM file (once sorted with samtools) an index can be built with sambamba index since --check-bins is off by default. Would it be possible to add an argument similar to --check-bins for sambamba sort?

For comparison, samtools sorts the same BAM file by leaving the bin incorrect.

[lomereiter]

The tools that write BAM now set the bin correctly prior to writing the records. The option like --check-bins doesn't make much sense when one can simply fix the records (index doesn't write BAM, so it can only check).

[tylo42]

Good point about fixing the records. I tested it out and it works beautifully. Thank you so much for your quick response and fix!