Change-O modifications to support 10X data

[Jason Vander Heiden]

1. Add definitions for LOCUS, C_CALL and CELL to the standard, with mappings to the appropriate AIRR Rearrangement fields (locus, c_call, cell_id)
2. Add parsing of LOCUS to change.IO.IMGTReader and change.IO.IHMMuneReader. Already complete for change.IO.IgBLASTReader.
3. Formalize paired cloning procedure. Ideally, as a separate subcommand to DefineClones that uses the CELL and FUNCTIONAL annotations to intelligently subset sequences for VH clustering, with either pre- or post-processing of clonal assignments using VL information.
4. CreateGermlines will also need a solution for how to generate consensus germlines for cloned and paired files.

[Jason Vander Heiden]

The --10x argument to MakeDb is overriding the IgBLAST LOCUS call. If we want to keep the 10X chain annotation, we should probably put it in a different field (eg, LOCUS_10X). Though, the 10X call use the correct nomenclature (eg, IGH) and the IgBLAST calls don't (eg, VH)...

[Roy Jiang]

1. Looks you already did that.

I would overwrite with IgBLAST. Seems easier to implement. But 2 needs to be done before we do this.

3/4. Steve wants to wait for more discussion on this.

Looks like you assigned to yourself so let me know if you need anything else from me.

[ssnn]

@Jason Vander Heiden we talked about this issue in the last meeting. We think the only point left is number 2:

Add parsing of LOCUS to change.IO.IMGTReader and change.IO.IHMMuneReader. Already complete for change.IO.IgBLASTReader

If this is correct, can we create a new issue for 2, and resolve this one?

[Jason Vander Heiden]

Looks like I took care of the locus thing about a year ago (42c0d6c).

If the plan is to deprecate DefineClones in favor of scoper, then we can just close this.

[ssnn]

See also #scoper/20 re deprecation of DefineClones, and #131 re “Maybe it would be better to make a MakeDb-airr command to parse any AIRR Rearrangement file and do a little standardization”. There’s commented out code in ConvertDb to add IMGT gaps, but it needs to be tested.

[Jason Vander Heiden]

Done enough.