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[ADAM-409][ADAM-520] Added local wigfix2bed tool #413

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merged 1 commit into from Dec 19, 2014

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laserson commented Oct 10, 2014

This does a local conversion from wigFix format to BED format. The Wiggle formats are exceptionally unsuited to Hadoop-style processing.

Fixes #409

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The build may fail bc it depends on @tdanford's gene-model PR.

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laserson commented Oct 10, 2014

The build may fail bc it depends on @tdanford's gene-model PR.

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GitHub pull request #413 of commit 8460362 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on test03.amplab (CentOS 6.5) (test03 centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/413/merge^{commit} # timeout=10Checking out Revision 0967be6 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 0967be6 > git rev-list c6703100935589fbf08b7dd7f62fa59728f34606 # timeout=10Triggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILURETest FAILed.

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GitHub pull request #413 of commit 8460362 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on test03.amplab (CentOS 6.5) (test03 centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/413/merge^{commit} # timeout=10Checking out Revision 0967be6 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 0967be6 > git rev-list c6703100935589fbf08b7dd7f62fa59728f34606 # timeout=10Triggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILURETest FAILed.

@@ -0,0 +1,57 @@
package org.bdgenomics.adam.cli

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Can you add the license header?

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Can you add the license header?

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+1, will re-review after #404 merges.

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fnothaft commented Oct 13, 2014

+1, will re-review after #404 merges.

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Also, need to add tests :)

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laserson commented Oct 14, 2014

Also, need to add tests :)

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GitHub pull request #413 of commit fe6c97b automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/413/merge^{commit} # timeout=10Checking out Revision b732ea4 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f b732ea4 > git rev-list 77ea367 # timeout=10Triggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILURE
Test FAILed.

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GitHub pull request #413 of commit fe6c97b automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/413/merge^{commit} # timeout=10Checking out Revision b732ea4 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f b732ea4 > git rev-list 77ea367 # timeout=10Triggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILURE
Test FAILed.

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Jenkins, retest this please.

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laserson commented Dec 14, 2014

Jenkins, retest this please.

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This now also fixes #520

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laserson commented Dec 14, 2014

This now also fixes #520

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@fnothaft ready for re-review. Also, I'm not sure if Jenkins respects me :(

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laserson commented Dec 14, 2014

@fnothaft ready for re-review. Also, I'm not sure if Jenkins respects me :(

@laserson laserson changed the title from [ADAM-409] Added local wigfix2bed tool to [ADAM-409][ADAM-520] Added local wigfix2bed tool Dec 14, 2014

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Actually, maybe Jenkins does like me!

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laserson commented Dec 14, 2014

Actually, maybe Jenkins does like me!

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Build result: FAILURE

GitHub pull request #413 of commit 59ae3d8 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/413/merge^{commit} # timeout=10Checking out Revision 5284de5ebde9075f74c9aa88e378b7441bbadefb (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 5284de5ebde9075f74c9aa88e378b7441bbadefb > git rev-list b1efbcd # timeout=10Triggering ADAM-prb ? 2.3.0,centosTriggering ADAM-prb ? 2.2.0,centosTriggering ADAM-prb ? 1.0.4,centosADAM-prb ? 2.3.0,centos completed with result SUCCESSADAM-prb ? 2.2.0,centos completed with result FAILUREADAM-prb ? 1.0.4,centos completed with result FAILURE
Test FAILed.

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GitHub pull request #413 of commit 59ae3d8 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/413/merge^{commit} # timeout=10Checking out Revision 5284de5ebde9075f74c9aa88e378b7441bbadefb (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 5284de5ebde9075f74c9aa88e378b7441bbadefb > git rev-list b1efbcd # timeout=10Triggering ADAM-prb ? 2.3.0,centosTriggering ADAM-prb ? 2.2.0,centosTriggering ADAM-prb ? 1.0.4,centosADAM-prb ? 2.3.0,centos completed with result SUCCESSADAM-prb ? 2.2.0,centos completed with result FAILUREADAM-prb ? 1.0.4,centos completed with result FAILURE
Test FAILed.

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GitHub pull request #413 of commit 993b2ad automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/413/merge^{commit} # timeout=10Checking out Revision e5235a5 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f e5235a5 > git rev-list b1efbcd # timeout=10Triggering ADAM-prb ? 2.3.0,centosTriggering ADAM-prb ? 2.2.0,centosTriggering ADAM-prb ? 1.0.4,centosADAM-prb ? 2.3.0,centos completed with result SUCCESSADAM-prb ? 2.2.0,centos completed with result FAILUREADAM-prb ? 1.0.4,centos completed with result FAILURE
Test FAILed.

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GitHub pull request #413 of commit 993b2ad automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/413/merge^{commit} # timeout=10Checking out Revision e5235a5 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f e5235a5 > git rev-list b1efbcd # timeout=10Triggering ADAM-prb ? 2.3.0,centosTriggering ADAM-prb ? 2.2.0,centosTriggering ADAM-prb ? 1.0.4,centosADAM-prb ? 2.3.0,centos completed with result SUCCESSADAM-prb ? 2.2.0,centos completed with result FAILUREADAM-prb ? 1.0.4,centos completed with result FAILURE
Test FAILed.

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Jenkins, retest this please.

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laserson commented Dec 14, 2014

Jenkins, retest this please.

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GitHub pull request #413 of commit 993b2ad automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/413/merge^{commit} # timeout=10Checking out Revision e5235a5 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f e5235a5 > git rev-list e5235a5 # timeout=10Triggering ADAM-prb ? 2.3.0,centosTriggering ADAM-prb ? 2.2.0,centosTriggering ADAM-prb ? 1.0.4,centosADAM-prb ? 2.3.0,centos completed with result SUCCESSADAM-prb ? 2.2.0,centos completed with result SUCCESSADAM-prb ? 1.0.4,centos completed with result FAILURE
Test FAILed.

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GitHub pull request #413 of commit 993b2ad automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/413/merge^{commit} # timeout=10Checking out Revision e5235a5 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f e5235a5 > git rev-list e5235a5 # timeout=10Triggering ADAM-prb ? 2.3.0,centosTriggering ADAM-prb ? 2.2.0,centosTriggering ADAM-prb ? 1.0.4,centosADAM-prb ? 2.3.0,centos completed with result SUCCESSADAM-prb ? 2.2.0,centos completed with result SUCCESSADAM-prb ? 1.0.4,centos completed with result FAILURE
Test FAILed.

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@fnothaft @tdanford finally passed the tests (though I didn't change anything). thoughts on merging?

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laserson commented Dec 18, 2014

@fnothaft @tdanford finally passed the tests (though I didn't change anything). thoughts on merging?

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I think it looks good, but Wiggle2Bed could use a bit more documentation. Can you document that up?

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fnothaft commented Dec 18, 2014

I think it looks good, but Wiggle2Bed could use a bit more documentation. Can you document that up?

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Like, some scaladoc?

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laserson commented Dec 18, 2014

Like, some scaladoc?

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Ja, exactly.

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fnothaft commented Dec 18, 2014

Ja, exactly.

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Apparently I also forgot to add it to ADAMMain

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laserson commented Dec 19, 2014

Apparently I also forgot to add it to ADAMMain

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@fnothaft k, added a bit of doc. I looked at the other CLI commands and they actually have very light scaladoc as well. Let me know if you think this is still insufficient.

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laserson commented Dec 19, 2014

@fnothaft k, added a bit of doc. I looked at the other CLI commands and they actually have very light scaladoc as well. Let me know if you think this is still insufficient.

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GitHub pull request #413 of commit 28778ff automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/413/merge^{commit} # timeout=10Checking out Revision b409bd0004a00c2dac712b5c567963b3e013c8e3 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f b409bd0004a00c2dac712b5c567963b3e013c8e3 > git rev-list aa866c4 # timeout=10Triggering ADAM-prb ? 2.3.0,centosTriggering ADAM-prb ? 2.2.0,centosTriggering ADAM-prb ? 1.0.4,centosADAM-prb ? 2.3.0,centos completed with result FAILUREADAM-prb ? 2.2.0,centos completed with result SUCCESSADAM-prb ? 1.0.4,centos completed with result FAILURE
Test FAILed.

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GitHub pull request #413 of commit 28778ff automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/413/merge^{commit} # timeout=10Checking out Revision b409bd0004a00c2dac712b5c567963b3e013c8e3 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f b409bd0004a00c2dac712b5c567963b3e013c8e3 > git rev-list aa866c4 # timeout=10Triggering ADAM-prb ? 2.3.0,centosTriggering ADAM-prb ? 2.2.0,centosTriggering ADAM-prb ? 1.0.4,centosADAM-prb ? 2.3.0,centos completed with result FAILUREADAM-prb ? 2.2.0,centos completed with result SUCCESSADAM-prb ? 1.0.4,centos completed with result FAILURE
Test FAILed.

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Jenkins, retest this please.

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fnothaft commented Dec 19, 2014

Jenkins, retest this please.

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LGTM; If there are no comments by midday tomorrow, I will merge.

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fnothaft commented Dec 19, 2014

LGTM; If there are no comments by midday tomorrow, I will merge.

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sg

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laserson commented Dec 19, 2014

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fnothaft added a commit that referenced this pull request Dec 19, 2014

Merge pull request #413 from laserson/wig
[ADAM-409][ADAM-520] Added local wigfix2bed tool

@fnothaft fnothaft merged commit 1ca67a5 into bigdatagenomics:master Dec 19, 2014

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Merged! Thanks @laserson!

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fnothaft commented Dec 19, 2014

Merged! Thanks @laserson!

@laserson laserson deleted the laserson:wig branch Dec 22, 2014

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