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Few transform tweaks #434

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merged 2 commits into from
Oct 29, 2014
Merged

Few transform tweaks #434

merged 2 commits into from
Oct 29, 2014

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fnothaft
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Fixes #432 and #433. Puts BQSR after indel realignment and makes it possible to dump BQSR observations to a file.

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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/313/
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@fnothaft
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Rebased.

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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/316/
Test PASSed.

tdanford added a commit that referenced this pull request Oct 29, 2014
@tdanford
Merge pull request #434 from fnothaft/realign-before-bqsr
854fc38 
Few transform tweaks
@tdanford tdanford merged commit 854fc38 into bigdatagenomics:master Oct 29, 2014
@fnothaft fnothaft mentioned this pull request Oct 29, 2014
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Indel realignment should happen before BQSR
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@fnothaft @AmplabJenkins @tdanford