Fix to deal with underscore in chromosome names in GRCh38 and to improve breakpoint merging
Description
Temporary files were created with underscore as seperator in file name but GRCh38 has chromosome names with underscore in them, resulting in exceptions when running qsv. Fixed to use a different separator in file names. Also identified some issues with merging of clip breakpoints and fixed these.
Type of change
[X] Bug fix (non-breaking change which fixes an issue)
How Has This Been Tested?
Added or updated new unit tests
Are WDL Updates Required?
Will need to do new adamajava release create wdlwf/wdl tags. Update sv.wdl and somaticDnaFastqToMaf.wdl
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
Fix to deal with underscore in chromosome names in GRCh38 and to improve breakpoint merging
Description
Temporary files were created with underscore as seperator in file name but GRCh38 has chromosome names with underscore in them, resulting in exceptions when running qsv. Fixed to use a different separator in file names. Also identified some issues with merging of clip breakpoints and fixed these.
Type of change
How Has This Been Tested?
Added or updated new unit tests
Are WDL Updates Required?
Will need to do new adamajava release create wdlwf/wdl tags. Update sv.wdl and somaticDnaFastqToMaf.wdl
Checklist: