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Vcf gz datatype #4254

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merged 13 commits into from Aug 10, 2017

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commented Jun 28, 2017

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commented Jun 28, 2017

@galaxybot test this

f.seek(offset)
ck_data = f.read(ck_size or trans.app.config.display_chunk_size)
if ck_data and ck_data[-1] != '\n':
f = compression_utils.get_fileobj(dataset.file_name)

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mvdbeek Jun 29, 2017

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I think we can do with compression_utils.get_fileobj(dataset.file_name) as f:.

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commented Jul 6, 2017

@ffinfo let me know if you want to continue working on this (I think we're almost there), otherwise I can do the last bit of polishing.

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commented Jul 6, 2017

@mvdbeek Ye was still planning to continue on this. I think I still have some uncommitted code for a test tool. Was a bit of a chaos when I did came back to Leiden. You know how that goes with todo's ;)

<param name="input" format="vcf_bgzip" type="data" label="Source file"/>
</inputs>
<outputs>
<data format="data" ftype="vcf_bgzip" name="output" />

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This should be format="vcf_bgzip". ftype is (confusingly ...) only used in the test section.

@ffinfo ffinfo changed the title WIP: Vcf gz datatype Vcf gz datatype Jul 6, 2017

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commented Jul 7, 2017

@galaxybot test this

mvdbeek and others added some commits Jun 27, 2017

Add VcfGz datatype
This adds support for uploading VcfGz files in the upload box. When a
user does this, the file will not be uncompressed. Also adds
uncompressed preview.

TODO:
  - Move Vcf class to BaseVcf
  - Vcf and VcfGz should both inherit from BaseVcf
  - Add a metadata element for VcfGz indexes (vzf.gz.tbi)
  - Create index (in set_meta method of VcfGz class)
  - Write test tools

This is a kcikstart to @ffinfo GCC hack project.

@mvdbeek mvdbeek force-pushed the ffinfo:vcf_gz_datatype branch from 2b83183 to 5cc71d2 Jul 7, 2017

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commented Jul 7, 2017

@galaxybot test this

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commented Aug 4, 2017

@ffinfo this is looking good to me, If you're happy with this I can merge it. bctools generates csi indexes by default (i.e without the -t flag), are these widely used ? Should we also implement them ?

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commented Aug 4, 2017

Well tools like Picard and GATK are using by default '.tbi' extensions. The csi is more used for bcf files and not for vcf files. That why I think it's better to keep it with the '-t' flag

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commented Aug 7, 2017

Alright, we can always add this if there is demand.

@mvdbeek mvdbeek removed the status/WIP label Aug 7, 2017

@mvdbeek mvdbeek force-pushed the ffinfo:vcf_gz_datatype branch from 13d32ee to 05e9cab Aug 7, 2017

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commented Aug 7, 2017

@galaxybot test this

@mvdbeek mvdbeek force-pushed the ffinfo:vcf_gz_datatype branch from 05e9cab to ed67b11 Aug 7, 2017

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commented Aug 7, 2017

@galaxybot test this

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commented Aug 10, 2017

Awesome - thanks for the contribution @ffinfo and @mvdbeek !

@jmchilton jmchilton merged commit bcdf2c8 into galaxyproject:dev Aug 10, 2017

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nsoranzo added a commit to nsoranzo/galaxy that referenced this pull request Aug 22, 2017

Fix `vcf_bgzip` datatype
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.
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