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Bcf.gz to bcf (and reverse) converters + bcf_bgzip data type #1148
Bcf.gz to bcf (and reverse) converters + bcf_bgzip data type #1148
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…med files to follow standard naming scheme
(options, args) = parser.parse_args() | ||
input_fname, output_fname = args | ||
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subprocess.call(["bcftools", "view", input_fname, "-o", output_fname, "-O", "u"]) |
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@markiskander can you please move this command directly into the tools. This way we completely save this file :)
Thanks @markiskander looks great! |
Thanks for the contribution @markiskander, I'm marking this as a "work in progress" until @bgruening's issues are addressed. Hope this is okay. |
Note @markiskander has finished his term and wont have time to work on this anymore. |
@bgruening Given @markiskander isn't available to modify these tools, can we just merge as is? This won't be the only converter with an unnecessary wrapper? |
AFAIK this follows the same general template as vcf_to_vcf_bgzip converter, which I had used as a reference for this. It's practically the same thing but with bcfs instead. |
I will fix my comments post merge, no problem! |
Bcf.gz to bcf (and reverse) converters + bcf_bgzip data type
…rters Since https://bitbucket.org/galaxy/galaxy-central/pull-requests/353 (only) compressed BCF files have been sniffed as `bcf`, so the `bcf_bgzip` datatype (introduced 2 years later in galaxyproject#1148 ) is an unused duplicate. This adds also a distinct `bcf_uncompressed` datatype (and converters) for the rare cases when it may be useful.
Hey guys. I added a bcf_bgzip datatype as well as converters for getting it converted to bcf (and from bcf to bcf_bgzip). I did my best to closely follow the existing naming schemes and coding styles. Let me know if there's anything else that needs to be done. Thanks!