This is not a code issue, but a documentation issue. The documentation does not talk about CRAM file format (at least, not the documentation for sambamba view), but running the command in the command line show parameters to manage this format.
In case you decide to keep suport for CRAM file format, it would be good to update the docs with the relevant information about CRAM.
pjotrp
commented
5 years ago
This is not a code issue, but a documentation issue. The documentation does not talk about CRAM file format (at least, not the documentation for sambamba view), but running the command in the command line show parameters to manage this format.
In case you decide to keep suport for CRAM file format, it would be good to update the docs with the relevant information about CRAM.