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Port single file BAM and header code to VCF #1009

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fnothaft opened this issue Apr 23, 2016 · 2 comments
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Port single file BAM and header code to VCF #1009

fnothaft opened this issue Apr 23, 2016 · 2 comments
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@fnothaft
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0.20.0

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@fnothaft
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I was looking over the VCF export code while working on #909 and noticed that we had a lot of cruft around setting the VCF headers. Also, we don't have code for writing out a single VCF file.
@fnothaft fnothaft self-assigned this Apr 23, 2016
@fnothaft fnothaft added this to the 0.20.0 milestone Apr 23, 2016
@heuermh
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heuermh commented Apr 24, 2016

We'll also need header + concat stuff for writing out a single IntervalList feature file.

@heuermh heuermh mentioned this issue May 18, 2016
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@ryan-williams
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Recent activity on #676 discusses the need for this in BAMs as well.

@heuermh heuermh mentioned this issue Jun 7, 2016
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@heuermh heuermh mentioned this issue Jun 28, 2016
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@fnothaft fnothaft mentioned this issue Aug 8, 2016
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fnothaft added a commit to fnothaft/adam that referenced this issue Aug 8, 2016
@fnothaft
[ADAM-1009] Port single file save code over to VCF.
4260568 
Factor single file save code out of AlignmentRecordRDD. Resolves bigdatagenomics#1009.
@fnothaft fnothaft mentioned this issue Aug 8, 2016
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fnothaft added a commit to fnothaft/adam that referenced this issue Aug 30, 2016
@fnothaft
[ADAM-1009] Port single file save code over to VCF.
838c2ad 
Factor single file save code out of AlignmentRecordRDD. Resolves bigdatagenomics#1009.
fnothaft added a commit to fnothaft/adam that referenced this issue Sep 6, 2016
@fnothaft
[ADAM-1009] Port single file save code over to VCF.
12df62d 
Factor single file save code out of AlignmentRecordRDD. Resolves bigdatagenomics#1009.
fnothaft added a commit to fnothaft/adam that referenced this issue Sep 7, 2016
@fnothaft
[ADAM-1009] Port single file save code over to VCF.
d5221a5 
Factor single file save code out of AlignmentRecordRDD. Resolves bigdatagenomics#1009.
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@heuermh @ryan-williams @fnothaft