.bai and .bam file conventions

[a-l-holmes]

Background
Typically files are updated with the index extension like filename.cram and filename.cram.crai and the whistle code extracts the latter file extension and references the cram file when creating a DocumentReference for the crai file. X01-Hakonarson and HTP both have files with .bam and .bai types that do not behave in the same way: there is a file.bam and a file.bai.

Scope
Make the code more flexible to handle any type of file and index file behavior.

Acceptance Criteria
Whistle code should be able to handle files with compounding file extensions and for file extensions on new files.