fix(qsv): qsv can now write CRAM files internally

[holmeso]

Description

qSV needs to be able to run with CRAM files. There were a few places where qSV was catering specifically foe SAM and BAM files, and this PR addresses that.
Removed references to "BLAT" in the logging (confusing seeing as BLAT is not used)

Type of change

Please delete options that are not relevant.

• New feature (non-breaking change which adds functionality)

How Has This Been Tested?

Additional unit tests, and code has been run and compared against older code to check for equality

Are WDL Updates Required?

no

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes