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Add quality score binner #1485

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merged 1 commit into from May 12, 2017

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fnothaft commented Apr 11, 2017

Resolves #1462. WIP. Still need to:

  • Add docs
  • Characterize
  • Add to fragment path
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Coverage Status

Coverage increased (+0.1%) to 81.785% when pulling 2d9cb2c on fnothaft:issues/1462-quality-score-binner into 93b32c6 on bigdatagenomics:master.

coveralls commented Apr 11, 2017

Coverage Status

Coverage increased (+0.1%) to 81.785% when pulling 2d9cb2c on fnothaft:issues/1462-quality-score-binner into 93b32c6 on bigdatagenomics:master.

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1485/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains d0fb3edd7021762f878ef7a5ab66ab37dd25c38e # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1485/merge^{commit} # timeout=10Checking out Revision d0fb3edd7021762f878ef7a5ab66ab37dd25c38e (origin/pr/1485/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f d0fb3edd7021762f878ef7a5ab66ab37dd25c38eFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Apr 11, 2017

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1485/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains d0fb3edd7021762f878ef7a5ab66ab37dd25c38e # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1485/merge^{commit} # timeout=10Checking out Revision d0fb3edd7021762f878ef7a5ab66ab37dd25c38e (origin/pr/1485/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f d0fb3edd7021762f878ef7a5ab66ab37dd25c38eFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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fnothaft Apr 11, 2017

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Jenkins, retest this please.

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fnothaft commented Apr 11, 2017

Jenkins, retest this please.

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Coverage Status

Coverage increased (+0.1%) to 81.785% when pulling 2d9cb2c on fnothaft:issues/1462-quality-score-binner into 93b32c6 on bigdatagenomics:master.

coveralls commented Apr 11, 2017

Coverage Status

Coverage increased (+0.1%) to 81.785% when pulling 2d9cb2c on fnothaft:issues/1462-quality-score-binner into 93b32c6 on bigdatagenomics:master.

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Test PASSed.
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Test PASSed.

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@heuermh

Looks good! Nice test coverage. Does it help performance much?

Show outdated Hide outdated adam-cli/src/main/scala/org/bdgenomics/adam/cli/Transform.scala Outdated
// if we have multiple bins, validate them
// - check that we don't have gaps between bins
// - check that we don't have overlapping bins
if (bins.size > 1) {

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heuermh Apr 12, 2017

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would this check be better in QualityScoreBin.apply?

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heuermh Apr 12, 2017

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would this check be better in QualityScoreBin.apply?

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heuermh May 3, 2017

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I'd be ok merging this with the doc string fix suggested above

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heuermh commented May 3, 2017

I'd be ok merging this with the doc string fix suggested above

@fnothaft fnothaft added this to the 0.23.0 milestone May 11, 2017

[ADAM-1462] Add quality score binner.
Resolves #1462. Adds an API for binning quality scores to `AlignmentRecordRDD`
and `FragmentRDD`. Exposes this on the `Transform` CLI.
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@heuermh addressed the doc issue. This is good to go from my side.

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fnothaft commented May 12, 2017

@heuermh addressed the doc issue. This is good to go from my side.

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Coverage Status

Coverage increased (+0.1%) to 82.015% when pulling a089670 on fnothaft:issues/1462-quality-score-binner into 0dd09b2 on bigdatagenomics:master.

coveralls commented May 12, 2017

Coverage Status

Coverage increased (+0.1%) to 82.015% when pulling a089670 on fnothaft:issues/1462-quality-score-binner into 0dd09b2 on bigdatagenomics:master.

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Test PASSed.
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Test PASSed.

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Test PASSed.
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@heuermh heuermh merged commit 18191f9 into bigdatagenomics:master May 12, 2017

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codacy/pr Not so good... This pull request quality could be better.
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coverage/coveralls Coverage increased (+0.1%) to 82.015%
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heuermh May 12, 2017

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Thank you, @fnothaft

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heuermh commented May 12, 2017

Thank you, @fnothaft

@fnothaft fnothaft deleted the fnothaft:issues/1462-quality-score-binner branch May 21, 2017

fnothaft added a commit to fnothaft/adam that referenced this pull request May 21, 2017

[ADAM-1359] Merge `reads2fragments` and `fragments2reads` into `trans…
…formFragments`

Resolves bigdatagenomics#1359. Also, propegates the quality score binner (bigdatagenomics#1485) up to the
`transformFragments` CLI.

fnothaft added a commit to fnothaft/adam that referenced this pull request May 26, 2017

[ADAM-1359] Merge `reads2fragments` and `fragments2reads` into `trans…
…formFragments`

Resolves bigdatagenomics#1359. Also, propegates the quality score binner (bigdatagenomics#1485) up to the
`transformFragments` CLI.

heuermh added a commit that referenced this pull request May 30, 2017

[ADAM-1359] Merge `reads2fragments` and `fragments2reads` into `trans…
…formFragments`

Resolves #1359. Also, propegates the quality score binner (#1485) up to the
`transformFragments` CLI.

@heuermh heuermh added this to Completed in Release 0.23.0 May 30, 2017

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