Fixes for VCF/BCF datatypes #4477
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…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.
In galaxyproject#4254 `vcf_bgzip` was made a proper datatype with the introduction of the `VcfGz` class, but was still described as a subclass in `datatypes_conf.xml` . Also fix `file_ext` attribute in `BaseVcf` and subclasses.
The `bcftools` binary is used by the `set_meta()` method of the `Bcf` datatype class. Having a `<requirement>` for it in the set_metadata tool makes it possible to use conda to resolve the dependency instead of forcing the admin to install `bcftools` on the PATH of the Galaxy user. This will also fix errors like https://travis-ci.org/galaxyproject/tools-iuc/jobs/266923024#L1994 when running ``` planemo test --conda_dependency_resolution --conda_auto_install ```
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bcf_bgzipdatatype tobcf. Since https://bitbucket.org/galaxy/galaxy-central/pull-requests/353 (only) compressed BCF files have been sniffed asbcf, so thebcf_bgzipdatatype (introduced 2 years later in Bcf.gz to bcf (and reverse) converters + bcf_bgzip data type #1148 ) is an unused duplicate.bcf_uncompresseddatatype (and converters) for the rare cases when it may be useful.vcf_bgzipdatatype. In Vcf gz datatype #4254vcf_bgzipwas made a proper datatype with the introduction of theVcfGzclass, but was still described as a subclass indatatypes_conf.xml. Also fixfile_extattribute inBaseVcfand subclasses.The
bcftoolsbinary is used by theset_meta()method of theBcfdatatype class. Having a<requirement>for it in the set_metadata tool makes it possible to use conda to resolve the dependency instead of forcing the admin to installbcftoolson the PATH of the Galaxy user.This will also fix errors like https://travis-ci.org/galaxyproject/tools-iuc/jobs/266923024#L1994 when running