Additional features to add to ConvertDb-genbank

[Jason Vander Heiden]

1. Add a flag to ConvertDb-genbank to retain invalid CDS (stop codon) records, but convert the JUNCTION annotation to a misc_feature.

2. Add arguments for sex and tissue-type specification.

3. AIRR formats support.

[Jason Vander Heiden]

1. Add COORDINATES type to inference qualifiers.
2. Use protein motif for inference qualifier in CDS (JUNCTION) and alignment for V, D, J and C segments.

[Jason Vander Heiden]

All of the above is done, except AIRR format support.

Also updated keywords to TLS; Targeted Locus Study; AIRR; MiAIRR:1.0.

[Jason Vander Heiden]

We could probably add the execution of tbl2asn as an optional post-processing step as well. It should only require adding:

1. Input of a template .sbt file generated via https://submit.ncbi.nlm.nih.gov/genbank/template/submission.
2. Arguments for BioProject and BioSample accession numbers.
3. An --exec argument to point to tbl2asn
4. A flag specifying whether or not to perform the step (--asn).

[Jason Vander Heiden]

AIRR format support added in 35caac8. At the time of writing, this is dependent upon the version of the AIRR standard in the Rearrangement-fields branch.

[Jason Vander Heiden]

Could use a small vignette/tutorial for this in the changeo docs.

[Jason Vander Heiden]

Added support for non-IMGT gene names and AIRR_READ_COUNT and AIRR_CELL_INDEX notes in 353afd1.

[Jason Vander Heiden]

Need to add support for passing all these various arguments via a yaml file instead of individually.

[Jason Vander Heiden]

YAML config argument done in c6e6b1e.

[Jason Vander Heiden]

tbl2asn execution added in af1ac5b.