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[ADAM-1359] Merge `reads2fragments` and `fragments2reads` into `transformFragments` #1543

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merged 1 commit into from May 30, 2017

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@fnothaft
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fnothaft commented May 21, 2017

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

@fnothaft fnothaft added this to the 0.23.0 milestone May 21, 2017

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Coverage Status

Coverage increased (+0.01%) to 82.053% when pulling 1532778 on fnothaft:issues/1359-transform-fragments into 2820e94 on bigdatagenomics:master.

coveralls commented May 21, 2017

Coverage Status

Coverage increased (+0.01%) to 82.053% when pulling 1532778 on fnothaft:issues/1359-transform-fragments into 2820e94 on bigdatagenomics:master.

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heuermh May 23, 2017

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Looks like we need to kill the current Jenkins job and try again. Will retest this please do the trick?

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heuermh commented May 23, 2017

Looks like we need to kill the current Jenkins job and try again. Will retest this please do the trick?

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Jenkins, retest this please.

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fnothaft commented May 23, 2017

Jenkins, retest this please.

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@heuermh there were some issues with Jenkins this weekend, so I'm guessing the build got killed during a Jenkins restart.

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fnothaft commented May 23, 2017

@heuermh there were some issues with Jenkins this weekend, so I'm guessing the build got killed during a Jenkins restart.

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Coverage Status

Coverage increased (+0.01%) to 82.053% when pulling 1532778 on fnothaft:issues/1359-transform-fragments into 2820e94 on bigdatagenomics:master.

coveralls commented May 23, 2017

Coverage Status

Coverage increased (+0.01%) to 82.053% when pulling 1532778 on fnothaft:issues/1359-transform-fragments into 2820e94 on bigdatagenomics:master.

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AmplabJenkins May 23, 2017

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2043/

Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1543/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 4b3b5db # timeout=10Checking out Revision 4b3b5db (origin/pr/1543/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 4b3b5db254faec34155b48fb15114570d365b186First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented May 23, 2017

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2043/

Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1543/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 4b3b5db # timeout=10Checking out Revision 4b3b5db (origin/pr/1543/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 4b3b5db254faec34155b48fb15114570d365b186First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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

Resolves #1359. Also, propegates the quality score binner (#1485) up to the
`transformFragments` CLI.
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coveralls May 26, 2017

Coverage Status

Coverage increased (+0.01%) to 82.053% when pulling 92fa66b on fnothaft:issues/1359-transform-fragments into 3ea4f18 on bigdatagenomics:master.

coveralls commented May 26, 2017

Coverage Status

Coverage increased (+0.01%) to 82.053% when pulling 92fa66b on fnothaft:issues/1359-transform-fragments into 3ea4f18 on bigdatagenomics:master.

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AmplabJenkins May 26, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2063/
Test PASSed.

AmplabJenkins commented May 26, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2063/
Test PASSed.

@heuermh heuermh merged commit b0c5c5f into bigdatagenomics:master May 30, 2017

2 of 3 checks passed

codacy/pr Not so good... This pull request quality could be better.
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coverage/coveralls Coverage increased (+0.01%) to 82.053%
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default Merged build finished.
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heuermh May 30, 2017

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Thank you, @fnothaft

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heuermh commented May 30, 2017

Thank you, @fnothaft

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

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