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bcftools_consensus has duplicate mask options #6546

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pvanheus opened this issue Nov 10, 2024 · 0 comments

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pvanheus commented Nov 10, 2024

The bcftools_consensus wrapper currently has two inputs for the --mask argument:

https://github.com/galaxyproject/tools-iuc/blob/main/tools/bcftools/bcftools_consensus.xml#L77 - which is a simple boolean
https://github.com/galaxyproject/tools-iuc/blob/main/tools/bcftools/bcftools_consensus.xml#L101 - which allows specifying the mask character and is currently unused.

I have created a fix for this (https://github.com/pvanheus/tools-iuc/blob/fix_duplicate_mask/tools/bcftools/bcftools_consensus.xml) but see that #6293 is currently open, so my fix should probably be applied on top of (a passing version of) that. I might find time to merge into that PR but in the meantime leaving this issue here as a reminder.

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