Add CRAM file support for IGV in study plugins

[mikkonie]

There is a request from @holtgrewe for adding .cram file support for IGV sessions. Spec forthcoming. If it's not too major, I'll get this in v0.14.2.

Spec

• Update study app methods to search for both .bam and .cram
  • TODO: List related methods here
• Ensure .cram files get inserted into generated IGV sessions
• Ensure .cram files are also properly found for study cache
• TBD: Extend SHEETS_IGV_OMIT_BAM and igv_omit_bam setting functionality to CRAM files?
  • If so, update GUI labels and setting spec
• Update GUI labels to reflect CRAM support
• Add tests
  • Test link retrieval
  • Test cache
  • Test IGV generation
  • Remember to test with both .bam and .cram (dummy) files, including combinations of both
• Update documentation

Tasks

• [x] Update cancer plugin and tests
• [x] Update germline plugin and tests
• [x] Update labels for BAM omit settings
• [x] Update GUI if needed Seems to be OK
• [x] Update documentation regarding BAM support
• [x] Update major changes doc with migrate info

[holtgrewe]

OK, here we go. For IGV it does not matter whether the file is a BAM or CRAM file so we can place CRAM everywhere we place BAM.

The current logic to identify the BAM file for a single sample/library

1. in the library directory, look for all files ending in .bam
2. sort this list lexicographically
3. use the last found one

This logic needs to be changed to (1) reads "in the library directory, look for all files ending in .bam or .cram.

That's all we need.

[mikkonie]

Done.