Create SAM strict specifications with exemplar validation and enforcement tools

[d-cameron]

GRIDSS is dying on invalid input data of various forms. Although the inputs are syntactically valid SAM files, they are semantically inconsistent. Particularly problematic are the SAM fields that contain redundant information that is stored in other SAM records (such as mate and split read fields and tags) as these can become out of sync.

• Create SAM strict specifications based on a superset of the SAM recommended practices
  • Contribute this back to the SAM specs
• Create command-line strict validation tool
• Create command-line strict enforcement tool
  • Output diagnostics with #records adjusted, #records deleted, #tags corrected, etc
  • superset of existing ComputeSamTags functionality

[d-cameron]

GRIDSS crashes when SA tag does not match SAM record