use chrX and chrY to match sex chromosomes #713
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The ploidy estimation script uses string comparison to "X" and "Y" to identify sex chromsomes, but the ploidy matrix input to the script uses "chrX" and "chrY" for the sex chromsomes. This commit updates the script to correctly identify sex chrosomomes.
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In a few places in the pipeline we provide chrX and chrY as inputs for this reason (example). Should we do this more consistently? |
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It's a better solution to have them as inputs but we only support hg38 anyway. Up to @CuriousTim if he wants to do that and re-test it. |
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I can add an input to the script. Should I also update the WDLs? |
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Yes please update the WDLs and include the allosome contig names as inputs. Have "chrX" and "chrY" as defaults. |
CuriousTim
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Update the ploidy estimation script and associated WDLs to accept a custom set of allosome contigs, with the default being chrX and chrY.
I think I'd prefer something like this where we explicitly pass X and Y as separate optional variables. |
Expose separate inputs to specify the allosomal contig names in PloidyEstimation with the defaults being "chrX" and "chrY".
The method to pass the names of the allosomes to PloidyEstimation was changed from passing a file to passing two strings, but some calling workflows were not updated to reflect the change. This commit fixes the inputs.
The ploidy estimation script uses string comparison to "X" and "Y" to identify sex chromsomes, but the ploidy matrix input to the script uses "chrX" and "chrY" for the sex chromsomes. This commit updates the script to correctly identify sex chrosomomes.