fix: add sd_locs_vcf_index input to SDtoBAF

broadinstitute / gatk-sv

A structural variation pipeline for short-read sequencing

BSD 3-Clause "New" or "Revised" License

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fix: add sd_locs_vcf_index input to SDtoBAF #644

Open simojoe opened 5 months ago

simojoe commented 5 months ago

Fixes #643

Adding the index in-place from the main file name.

I have not found any other reference to SDtoBAF that needs to be updated.

VJalili commented 5 months ago

@simojoe, thank you for fixing this! Optional index files can be confusing, and your suggested fix fits perfectly with what we discussed in https://github.com/broadinstitute/gatk-sv/issues/578.

I want to suggest an improvement on your approach; can you please add an optional input sd_locs_vcf_index to the WDL, such that, if sv_locs_vcf is given, the sd_locs_vcf_index should also be given, and if sd_locs_vcf_index is not given, then infer it from sv_locs_vcf.