HKU-BAL/Clair3

Bump Whatshap to v1.7?

SamStudio8 opened this issue · 4 comments

SamStudio8 commented

Clair3 pins WhatsHap at version 1.4 and is missing out on some performance improvements, particularly related to the haplotag step. Would it be appropriate to bump the version in the package and distribute a new version of Clair3 to conda with WhatsHap 1.7 pinned?

aquaskyline commented

Bumping up WhatsHap to 1.7 in the next release. Any idea if this issue #163 (Error while opening BGZF compressed FASTA reference file) is also fixed in the new WhatsHap?

SamStudio8 commented

@aquaskyline Much appreciated! Looks like the underlying issue in #163 is from WhatsHap's use of pyfaidx which still raises that error for gzipped files. Sorry I'd misread the issue you'd linked there, it sadly does still seem to be an open issue on pyfaidx...

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zhengzhenxian commented

@SamStudio8 Bumped up "WhatsHap" version to 1.7 in v1.0.1, thanks!

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SamStudio8 commented

Thanks! I can confirm I'm seeing WhatsHap 1.7 installed from the Clair3 bioconda package now.