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[ADAM-1328] Rename `Transform` to `TransformAlignments`. #1521

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merged 1 commit into from May 21, 2017

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fnothaft commented May 12, 2017

Resolves #1328.

@fnothaft fnothaft requested a review from heuermh May 12, 2017

@fnothaft fnothaft added this to the 0.23.0 milestone May 12, 2017

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Coverage Status

Coverage decreased (-0.03%) to 81.849% when pulling 12d624c on fnothaft:issues/1328-rename-transform-alignments into 0dd09b2 on bigdatagenomics:master.

coveralls commented May 12, 2017

Coverage Status

Coverage decreased (-0.03%) to 81.849% when pulling 12d624c on fnothaft:issues/1328-rename-transform-alignments into 0dd09b2 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/1521/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 689e930 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1521/merge^{commit} # timeout=10Checking out Revision 689e930 (origin/pr/1521/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 689e93078b8ef1991429f3457a569e05c1a3e02bFirst 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 May 12, 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/1521/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 689e930 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1521/merge^{commit} # timeout=10Checking out Revision 689e930 (origin/pr/1521/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 689e93078b8ef1991429f3457a569e05c1a3e02bFirst 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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Jenkins, retest this please.

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fnothaft commented May 12, 2017

Jenkins, retest this please.

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Coverage Status

Coverage decreased (-0.03%) to 81.849% when pulling 12d624c on fnothaft:issues/1328-rename-transform-alignments into 0dd09b2 on bigdatagenomics:master.

coveralls commented May 12, 2017

Coverage Status

Coverage decreased (-0.03%) to 81.849% when pulling 12d624c on fnothaft:issues/1328-rename-transform-alignments into 0dd09b2 on bigdatagenomics:master.

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1992/

Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1521/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 689e930 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1521/merge^{commit} # timeout=10Checking out Revision 689e930 (origin/pr/1521/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 689e93078b8ef1991429f3457a569e05c1a3e02bFirst 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 May 12, 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/1992/

Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1521/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 689e930 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1521/merge^{commit} # timeout=10Checking out Revision 689e930 (origin/pr/1521/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 689e93078b8ef1991429f3457a569e05c1a3e02bFirst 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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Thanks @heuermh ; just fixed.

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fnothaft commented May 12, 2017

Thanks @heuermh ; just fixed.

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1994/

Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1521/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 0b21d34cad7c8be40c8918101a7f7fbed4b0a7b7 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1521/merge^{commit} # timeout=10Checking out Revision 0b21d34cad7c8be40c8918101a7f7fbed4b0a7b7 (origin/pr/1521/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 0b21d34cad7c8be40c8918101a7f7fbed4b0a7b7First 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 FAILUREADAM-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 FAILUREADAM-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 FAILUREADAM-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 FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented May 12, 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/1994/

Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1521/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 0b21d34cad7c8be40c8918101a7f7fbed4b0a7b7 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1521/merge^{commit} # timeout=10Checking out Revision 0b21d34cad7c8be40c8918101a7f7fbed4b0a7b7 (origin/pr/1521/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 0b21d34cad7c8be40c8918101a7f7fbed4b0a7b7First 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 FAILUREADAM-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 FAILUREADAM-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 FAILUREADAM-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 FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Coverage Status

Coverage decreased (-0.03%) to 81.983% when pulling 0f9f291 on fnothaft:issues/1328-rename-transform-alignments into 18191f9 on bigdatagenomics:master.

coveralls commented May 12, 2017

Coverage Status

Coverage decreased (-0.03%) to 81.983% when pulling 0f9f291 on fnothaft:issues/1328-rename-transform-alignments into 18191f9 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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Test PASSed.

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@heuermh can you merge?

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fnothaft commented May 18, 2017

@heuermh can you merge?

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I was thinking of pinging folks downstream about this one and #1532 to make sure the CLI changes don't cause too much trouble. I'll do that tomorrow.

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heuermh commented May 18, 2017

I was thinking of pinging folks downstream about this one and #1532 to make sure the CLI changes don't cause too much trouble. I'll do that tomorrow.

@heuermh heuermh merged commit 2820e94 into bigdatagenomics:master May 21, 2017

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coverage/coveralls Coverage decreased (-0.03%) to 81.983%
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codacy/pr Good work! A positive pull request.
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Thank you, @fnothaft!

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heuermh commented May 21, 2017

Thank you, @fnothaft!

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

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