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Bump Whatshap to v1.7? #193

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SamStudio8 opened this issue Apr 19, 2023 · 4 comments
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Bump Whatshap to v1.7? #193

SamStudio8 opened this issue Apr 19, 2023 · 4 comments
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enhancement New feature or request

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@SamStudio8
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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?
@SamStudio8 SamStudio8 changed the title Bump Whathap to >=1.7? Bump Whathap to v1.7? Apr 19, 2023
@SamStudio8 SamStudio8 changed the title Bump Whathap to v1.7? Bump Whatshap to v1.7? Apr 19, 2023
@aquaskyline
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aquaskyline commented Apr 20, 2023 •
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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?

@aquaskyline aquaskyline added the enhancement New feature or request label Apr 20, 2023
@SamStudio8
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SamStudio8 commented Apr 20, 2023 •
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@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...

sujunhao added a commit to HKU-BAL/Clair3-Trio that referenced this issue Apr 25, 2023
@sujunhao
*v0.6 (April 25, 2023)*: Upgraded Python 3.6 to 3.9. Upgraded Whatsha…
a24629e 
…p to [v1.7](HKU-BAL/Clair3#193). Fix gVCF format [error](#3). Added and [fixed](#4) "--enable_phasing" support. and "--enable_output_phasing" and "enable_output_haplotagging" supports.
@zhengzhenxian
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@SamStudio8 Bumped up "WhatsHap" version to 1.7 in v1.0.1, thanks!

@SamStudio8
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Thanks! I can confirm I'm seeing WhatsHap 1.7 installed from the Clair3 bioconda package now.

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@aquaskyline @SamStudio8 @zhengzhenxian