Enhancements to VCF save #1232

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fnothaft opened this Issue Oct 28, 2016 · 1 comment

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fnothaft commented Oct 28, 2016

We should add:

  • sort by reference index (we do sort by lex reference)
  • gzip when merging sharded files
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fnothaft Nov 7, 2016

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I was thinking about the second one a bit more, and actually, if we merge gzip'ed blocks, then that's valid gzip, right? If so, then it doesn't really make sense to add code to gzip on merge.

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fnothaft commented Nov 7, 2016

I was thinking about the second one a bit more, and actually, if we merge gzip'ed blocks, then that's valid gzip, right? If so, then it doesn't really make sense to add code to gzip on merge.

fnothaft added a commit to fnothaft/adam that referenced this issue Nov 7, 2016

[ADAM-1232] Default to contig order sort when saving sorted VCF.
Resolves #1232. Adds ability to select between lexicographic and contig index
sort order when saving a sorted VCF file.

fnothaft added a commit to fnothaft/adam that referenced this issue Nov 8, 2016

[ADAM-1232] Default to contig order sort when saving sorted VCF.
Resolves #1232. Adds ability to select between lexicographic and contig index
sort order when saving a sorted VCF file.

@heuermh heuermh closed this in 480c23e Nov 8, 2016

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