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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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fnothaft commented Apr 23, 2016

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

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heuermh Apr 24, 2016

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

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heuermh commented Apr 24, 2016

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

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ryan-williams May 18, 2016

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Recent activity on #676 discusses the need for this in BAMs as well.

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ryan-williams commented May 18, 2016

Recent activity on #676 discusses the need for this in BAMs as well.

@heuermh heuermh referenced this issue Jun 7, 2016

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Release ADAM version 0.20.0 #1048

47 of 61 tasks complete

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

[ADAM-1009] Port single file save code over to VCF.
Factor single file save code out of AlignmentRecordRDD. Resolves #1009.

fnothaft added a commit to fnothaft/adam that referenced this issue Aug 30, 2016

[ADAM-1009] Port single file save code over to VCF.
Factor single file save code out of AlignmentRecordRDD. Resolves #1009.

fnothaft added a commit to fnothaft/adam that referenced this issue Sep 6, 2016

[ADAM-1009] Port single file save code over to VCF.
Factor single file save code out of AlignmentRecordRDD. Resolves #1009.

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

[ADAM-1009] Port single file save code over to VCF.
Factor single file save code out of AlignmentRecordRDD. Resolves #1009.

@heuermh heuermh closed this in #1104 Sep 7, 2016

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