This change allows qsv to be used with the GRCh38 reference genome. It was previously hard-coded to
run against GRCh37
The chromosome positions map that is used by the tiled aligner is now built up from the reference index file.
The reference index file can be specified in the ini file that is passed to qsv (reference_index in general section).
If the reference file is not specified in the ini file, an attempt to locate it will be made by examining the reference file. If the index is in the same directory as the reference file, has the same name as the reference file and ends with .fai then it will be used.
Otherwise an exception will be thrown.
Type of change
Please delete options that are not relevant.
[X] Bug fix (non-breaking change which fixes an issue)
[X] New feature (non-breaking change which adds functionality)
[X] This change requires a documentation update
How Has This Been Tested?
Existing unit tests pass.
Additional unit tests have been created and pass
Are WDL Updates Required?
Although WDL updates are not required, if the reference index is not sitting next to the reference file and correctly named, qsv will not pick it up and an exception will be thrown.
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
Description
This change allows
qsvto be used with the GRCh38 reference genome. It was previously hard-coded to run against GRCh37The chromosome positions map that is used by the tiled aligner is now built up from the reference index file. The reference index file can be specified in the ini file that is passed to qsv (
reference_indexingeneralsection). If the reference file is not specified in the ini file, an attempt to locate it will be made by examining the reference file. If the index is in the same directory as the reference file, has the same name as the reference file and ends with.faithen it will be used. Otherwise an exception will be thrown.Type of change
Please delete options that are not relevant.
How Has This Been Tested?
Existing unit tests pass. Additional unit tests have been created and pass
Are WDL Updates Required?
Although WDL updates are not required, if the reference index is not sitting next to the reference file and correctly named,
qsvwill not pick it up and an exception will be thrown.Checklist: