Fix file naming of matepair file tmp files from underscore to "xxx" due to chrUn scaffold contigs in GRCh38
Description
Bugfix. For GRCh38, temporary matepair files names separated reference name from file ending with an underscore, but scaffold contigs in GRCh38 also have an underscore, so mate pairs were incorrectly matched. Changed file name to include "xxx"
Type of change
[X] Bug fix (non-breaking change which fixes an issue)
How Has This Been Tested?
Added unit tests and tested previously failing sample
Are WDL Updates Required?
sv.wdl will need to be updated to a new release of adamajava to include this change.
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 file naming of matepair file tmp files from underscore to "xxx" due to chrUn scaffold contigs in GRCh38
Description
Bugfix. For GRCh38, temporary matepair files names separated reference name from file ending with an underscore, but scaffold contigs in GRCh38 also have an underscore, so mate pairs were incorrectly matched. Changed file name to include "xxx"
Type of change
How Has This Been Tested?
Added unit tests and tested previously failing sample
Are WDL Updates Required?
sv.wdl will need to be updated to a new release of adamajava to include this change.
Checklist: