fix(qannotate): restore default value for HOM in confidence mode

[holmeso]

Description

Default value for HOM in confidence mode was erroneously changed in a recent PR ( #347).

This PR fixes that mistake by introducing another option homCutoff that is specifically used for the confidence mode to determine the number of homopolymers that are required to trigger a HOM value in the filter field.

And so, the options pertaining to homopolymers are now:

homWindow - sets the window size, used by HomopolymerMode, default is 100 homReportWindow - sets the window size that is included in the vcf info field. Used by HompolymersMode, default is 10 homCutoff - sets the nmber of homopolymers required to add the HOM annotation to the filter field. USed by ConfidenceMode, default is 6.

Type of change

Please delete options that are not relevant.

• [X] Bug fix (non-breaking change which fixes an issue)

How Has This Been Tested?

Added some unit tests. Ran code against vcf files generated by version 130 of code, and ouputs were the same (when default values were used).

Are WDL Updates Required?

nope

Checklist:

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