The code that loads the chromosome information from the index file was using the start offset in the index rather than the end of the previous chromosome + 1.
The tiled aligner file is built to use the previous chromosome + 1.
This led to gaps in the positions, which caused NPE.
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?
Existing tests pass, new tests check for NPE and that loading from index gives same result as loading from static list.
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
The code that loads the chromosome information from the index file was using the start offset in the index rather than the end of the previous chromosome + 1. The tiled aligner file is built to use the previous chromosome + 1.
This led to gaps in the positions, which caused NPE.
Type of change
Please delete options that are not relevant.
How Has This Been Tested?
Existing tests pass, new tests check for NPE and that loading from index gives same result as loading from static list.
Are WDL Updates Required?
no
Checklist: