In TiledAlignerUtil.loadReferenceIndexMap a check is performed on the supplied index file. If this is null, an attempt to locate the index file is then done based on the reference file. If this is found then that should be used.
Unfortunately the code was using the supplied index value (which was null) rather than the located index file (not null).
This was introduced in PR #313
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?
New test added, existing tests pass
Are WDL Updates Required?
No
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] 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
Description
In
TiledAlignerUtil.loadReferenceIndexMapa check is performed on the supplied index file. If this is null, an attempt to locate the index file is then done based on the reference file. If this is found then that should be used. Unfortunately the code was using the supplied index value (which was null) rather than the located index file (not null).This was introduced in PR #313
Type of change
Please delete options that are not relevant.
How Has This Been Tested?
New test added, existing tests pass
Are WDL Updates Required?
No
Checklist: