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Modifying conversion code to resolve #112. #260

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merged 1 commit into from Jun 9, 2014

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fnothaft commented Jun 7, 2014

Resolves #112. Specifically:

  • Adds code to SAM->ADAM conversion to only set mapping flags if the record is mapped.
  • Adds fields to the ADAMRecord to disambiguate secondary vs. supplementary alignments
  • Adds accompanying code to the ADAM->SAM conversion to ensure that secondary vs. supplementary alignments are properly converted back to SAM.
  • Updates DecadentRead to add the requirement statement that was removed because of #112.
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All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/352/

AmplabJenkins commented Jun 8, 2014

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/352/

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I merged another of your PR's, so don't forget to rebase this one!

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tdanford commented Jun 8, 2014

I merged another of your PR's, so don't forget to rebase this one!

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@tdanford rebased!

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fnothaft commented Jun 8, 2014

@tdanford rebased!

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All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/356/

AmplabJenkins commented Jun 8, 2014

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/356/

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All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/359/

AmplabJenkins commented Jun 8, 2014

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/359/

tdanford added a commit that referenced this pull request Jun 9, 2014

Merge pull request #260 from fnothaft/sanity-check-flags
Modifying conversion code to resolve #112.

@tdanford tdanford merged commit 596eae3 into bigdatagenomics:master Jun 9, 2014

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Thanks, Frank!

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tdanford commented Jun 9, 2014

Thanks, Frank!

@fnothaft fnothaft deleted the fnothaft:sanity-check-flags branch Jul 10, 2014

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