Maybe merge extended field arguments in MakeDb

Issue #148 resolved
Jason Vander Heiden created an issue

We currently have several arguments for adding a more verbose column set to the output of MakeDb (--scores, --regions, --cdr3,--junction) and there seems to be little reason to not specify all of them if you specify one. Also, I think we may need a similar option for the 10X annotations to be able to copy over, but not replace, the locus and gene calls.

It would be a backwards incompatible change, but it might be worth it to merge all such options into an --extended flag, such that we have a single “verbose output” argument that isn’t dependent upon the input files or subcommand.

Comments (2)

  1. Jason Vander Heiden reporter

    Unless anyone has any objections to this, I think I’m going to go ahead and do it prior to the format conversion.

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