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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.
The text was updated successfully, but these errors were encountered:
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).
I have a BAM where the bin was set incorrectly. When running
sambamba sort
the following error message is printed and sorting is aborted: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
forsambamba sort
?For comparison, samtools sorts the same BAM file by leaving the bin incorrect.
The text was updated successfully, but these errors were encountered: