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Save compressed single file VCF via HadoopBAM #1554

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heuermh opened this issue May 31, 2017 · 0 comments
Closed

Save compressed single file VCF via HadoopBAM #1554

heuermh opened this issue May 31, 2017 · 0 comments
Milestone
0.23.0

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@heuermh
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heuermh commented May 31, 2017

See comment #1532 (comment)
fnothaft added a commit to fnothaft/adam that referenced this issue Jul 16, 2017
@fnothaft
[ADAM-1554] Support saving BGZF VCF output.
5cce59e 
Resolves bigdatagenomics#1554. Additionally:

* Moves VCF file extension logic into ADAM, since Hadoop-BAM does not recognize
  .bgzf as a valid BGZF extension
* Refactored VCF output formats to remove need for ADAMHeaderlessVCFOutputFormat
@fnothaft fnothaft mentioned this issue Jul 17, 2017
Merged
fnothaft added a commit to fnothaft/adam that referenced this issue Jul 17, 2017
@fnothaft
[ADAM-1554] Support saving BGZF VCF output.
55d1af7 
Resolves bigdatagenomics#1554. Additionally:

* Moves VCF file extension logic into ADAM, since Hadoop-BAM does not recognize
  .bgzf as a valid BGZF extension
* Refactored VCF output formats to remove need for ADAMHeaderlessVCFOutputFormat
heuermh pushed a commit that referenced this issue Jul 17, 2017
@fnothaft @heuermh
[ADAM-1554] Support saving BGZF VCF output.
406d1e3 
Resolves #1554. Additionally:

* Moves VCF file extension logic into ADAM, since Hadoop-BAM does not recognize
  .bgzf as a valid BGZF extension
* Refactored VCF output formats to remove need for ADAMHeaderlessVCFOutputFormat
@heuermh heuermh modified the milestone: 0.23.0 Jul 22, 2017
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