Bump Whatshap to v1.7?

[SamStudio8]

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]

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]

@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...

[zhengzhenxian]

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

[SamStudio8]

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

[mdshw5]

@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...

I want to mention that I've finished work on mdshw5/pyfaidx#164 which should fix the issues related to indexing bgzipped FASTA files in pyfaidx. If you're able to test the new code before I merge and release a new stable version I'd be extremely grateful. Sorry for taking so long to get back to working on this issue, and thanks for your patience!

[zhengzhenxian]

@mdshw5

Thank you for the update! We have tested the new pyfaidx release locally, and it works properly with the bgzip reference using WhatsHap. We will include it in our next release.

[mdshw5]

Great! I’ll update here soon when I’ve made a new release.

[mdshw5]

This is now fixed, tested and released in pyfaidx v0.9.0!