Multiinfo

[chrisamiller]

overhauls vcf-info-annotator:

• Multi-column annotation (--column-mappings / -m)
  old: accepted a single info_field argument with separate -f/-d flags for format and description.
  new: -m/--column-mappings flag that accepts a comma-separated list of source_col:info_field:type:description mapping
  allows multiple TSV columns to be written to multiple INFO fields. Source and version metadata can optionally be appended as 5th and 6th colon-separated fields

• TSV format now requires a header row.

• does some sanity checking on fields in coerce_value

  • empty string pass through as "."
  • NA/NaN/Inf values handled appropriately
  • entries that can't be coerced will cause a crash ("red" can't be coerced to integer)

Points for discussion:

• change in how overwrite works:

  • previously, retained the original INFO header line, now replaces with the definition in arguments
  • adds a --clear-existing flag that works with --overwrite. If just --overwrite is specified, existing annotations from positions not in the new tsv file are retained. If --overwrite and --clear-existing are specified, existing annotations that don't match with positions in the new file are removed

• Reverse compatibility is broken - if we keep these changes, we'll have to update some pipelines downstream. We could shoehorn in a way to maintain the old behavior, but this felt cleaner. We should talk, though!

[chrisamiller]

This would close #46 (though in a slightly more complex way)

Also, the tests are going to continue to fail until PR #86 is merged