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Redesign HTSJDK3 vcf package to support codec/header versioning #2601

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cmnbroad opened this issue Apr 14, 2017 · 2 comments
Open

Redesign HTSJDK3 vcf package to support codec/header versioning #2601

cmnbroad opened this issue Apr 14, 2017 · 2 comments
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HTSJDK HTSJDK3
Milestone
Engine-Q12019

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@cmnbroad
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The VCFHeader and header line hierarchy classes in htsjdk need refactoring to fix a number of bugs, and to support clean handling of new versions of VCF and BCF. This work is mostly done, PR is here.
@cmnbroad cmnbroad self-assigned this Apr 14, 2017
@cmnbroad cmnbroad modified the milestones: 4.0 release, beta Apr 14, 2017
@droazen droazen modified the milestones: 4.0 release, beta May 30, 2017
@cmnbroad
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cmnbroad commented Aug 7, 2017

Note the fix for this (samtools/htsjdk#835) also fixes samtools/htsjdk#934, so we should try to get it in.

@droazen droazen modified the milestones: Engine-4.0, Engine-4.1 Oct 17, 2017
@droazen droazen added the HTSJDK3 label Oct 4, 2018
@droazen droazen modified the milestones: Engine-2Q2018, Engine-Q42018 Oct 4, 2018
@droazen droazen changed the title Refactor HTSJDK vcf package to support codec/header versioning Redesign HTSJDK3 vcf package to support codec/header versioning Oct 4, 2018
@magicDGS
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I think that it will be much better to do it at the codec level for any kind of record. Tracked in htsjdk3 in samtools/htsjdk-next-beta#30

@droazen droazen modified the milestones: Engine-Q42018, Engine-Q12019 Feb 4, 2019
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@droazen @magicDGS @cmnbroad