feat: add BZIP2 (.bz2) support for reading fasta and fastq #185
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G'day @tshauck does this PR look okay? Keen to get it merged so I can support reading .bz2 files ... |
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Hi @nickzoic, thanks for contributing this and apologies for the long delay! I ran the tests, and it looks like there's an unrelated issue I'll need to fix, before this can merge. I'll try to take care if over the next couple of days and follow up here when I know more. |
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Oh good because I have no idea what that error is meant to be about! |
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@nickzoic Thanks again for opening the PR! Would you mind rebasing your branch. I think then the test should be resolved and I can merge it. I could also apply the patch manually, but wouldn't maintain history as well in github. |
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I think I've now successfully wrestled git into doing what I meant :-) |
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@nickzoic Looks great, thanks! Merging then'll make a new biobear release. |
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@nickzoic The new build should now be on pypi (https://pypi.org/project/biobear/0.23.2/) -- would you mind giving it a try whenever you have time. Thanks again for the PR! |
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Yep! Upgraded to 0.23.2 via pypi, now it opens .fastq.bz2 and .fa.bz2 files no problem. Thanks! |
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Awesome, thanks! |
Adds "BZIP2" compression option for reading .fastq and .fasta files which happen to be compressed with BZIP2.
(Exon already supports this, this just makes that ability available in biobear)