[ADAM-848] TwoBitFile now support nBlocks and maskBlocks #850

laserson · 2015-10-06T07:35:42Z

Fixes #848.

AmplabJenkins · 2015-10-06T07:51:56Z

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fnothaft · 2015-10-06T13:24:59Z

adam-core/src/main/scala/org/bdgenomics/adam/rdd/BroadcastRegionJoin.scala

@@ -165,7 +165,7 @@ object BroadcastRegionJoin extends RegionJoin {
 *
 * @param regions The input-set of regions.
 */
-private[rdd] class NonoverlappingRegions(regions: Iterable[ReferenceRegion]) extends Serializable {


Why are we making these public? IMO, they should stay package private or move to the org.bdgenomics.adam.models package.

Yeah, couldn't decide what to do with this. models doesn't exactly seem like the right place for it IMO either, since it's used more like a utility for things. What about org.bdgenomics.adam.util?

I mean, it is a model, right? Mostly just a container with an invariant (regions shouldn't overlap).

lol, true. k, I'll move it there...

fnothaft · 2015-10-06T13:26:49Z

Other than nits around packaging, LGTM!

laserson · 2015-10-06T21:45:26Z

Ok, ready for squash and merge if you are.

laserson · 2015-10-06T21:45:38Z

(and rebase)

fnothaft · 2015-10-06T21:49:36Z

That sounds good! Can you squash and rebase and I will merge?

fnothaft · 2015-10-06T21:59:26Z

adam-core/src/main/scala/org/bdgenomics/adam/models/NonoverlappingRegions.scala

@@ -0,0 +1,194 @@
+package org.bdgenomics.adam.models


Also, add the license header. (You can do this with ./scripts/format-source).

My favorite script :) Haven't run that guy in a while

AmplabJenkins · 2015-10-06T22:01:43Z

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AmplabJenkins · 2015-10-06T22:02:43Z

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Build result: FAILURE

GitHub pull request #850 of commit bada988.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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 bada988^{commit} # timeout=10 > git branch -a --contains bada988 # timeout=10Checking out Revision bada988 () > git config core.sparsecheckout # timeout=10 > git checkout -f bada9887a500190cce8a38cf4fb1499263ccaf23First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2015-10-06T22:02:48Z

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GitHub pull request #850 of commit 3be2dcf.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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 3be2dcf^{commit} # timeout=10 > git branch -a --contains 3be2dcf # timeout=10Checking out Revision 3be2dcf () > git config core.sparsecheckout # timeout=10 > git checkout -f 3be2dcfd349f1f5bead880f30e09e18ddcf88793First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2015-10-06T22:02:54Z

Test FAILed.
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Build result: FAILURE

GitHub pull request #850 of commit 1f23804.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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 1f23804^{commit} # timeout=10 > git branch -a --contains 1f23804 # timeout=10 > git rev-parse remotes/origin/pr/850/head^{commit} # timeout=10Checking out Revision 1f23804 (origin/pr/850/head) > git config core.sparsecheckout # timeout=10 > git checkout -f 1f23804 > git rev-list 877caa3 # timeout=10Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

laserson · 2015-10-06T22:08:47Z

Jenkins, retest this please

laserson · 2015-10-06T22:11:40Z

We should be good to go on this one.

AmplabJenkins · 2015-10-06T22:18:12Z

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AmplabJenkins · 2015-10-06T22:18:58Z

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Build result: FAILURE

GitHub pull request #850 of commit 848f24b automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/850/merge^{commit} # timeout=10 > git branch -a --contains 34ee141140505b0d37847d1164a15486bece51ce # timeout=10 > git rev-parse remotes/origin/pr/850/merge^{commit} # timeout=10Checking out Revision 34ee141140505b0d37847d1164a15486bece51ce (origin/pr/850/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 34ee141140505b0d37847d1164a15486bece51ceFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

laserson · 2015-10-06T22:48:33Z

Jenkins, retest this please

AmplabJenkins · 2015-10-06T23:04:08Z

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Build result: FAILURE

[...truncated 16 lines...] > git rev-list 34ee141140505b0d37847d1164a15486bece51ce # timeout=10Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.2.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.3.1,centosTriggering ADAM-prb ? 1.0.4,2.10,1.2.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.2.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 1.0.4,2.11,1.2.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosADAM-prb ? 2.3.0,2.11,1.2.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 1.0.4,2.10,1.2.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.2.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 1.0.4,2.11,1.2.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

laserson · 2015-10-06T23:11:45Z

Jenkins, retest this please

laserson · 2015-10-06T23:16:04Z

Jenkins, retest this please

AmplabJenkins · 2015-10-06T23:19:06Z

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Build result: FAILURE

GitHub pull request #850 of commit c6c9919 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/850/merge^{commit} # timeout=10 > git branch -a --contains 71d4c282501eaf9ce360a3820e8278d30233b5f1 # timeout=10 > git rev-parse remotes/origin/pr/850/merge^{commit} # timeout=10Checking out Revision 71d4c282501eaf9ce360a3820e8278d30233b5f1 (origin/pr/850/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 71d4c282501eaf9ce360a3820e8278d30233b5f1 > git rev-list 34ee141140505b0d37847d1164a15486bece51ce # timeout=10Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2015-10-06T23:19:40Z

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Build result: FAILURE

GitHub pull request #850 of commit c6c9919 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/850/merge^{commit} # timeout=10 > git branch -a --contains 71d4c282501eaf9ce360a3820e8278d30233b5f1 # timeout=10 > git rev-parse remotes/origin/pr/850/merge^{commit} # timeout=10Checking out Revision 71d4c282501eaf9ce360a3820e8278d30233b5f1 (origin/pr/850/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 71d4c282501eaf9ce360a3820e8278d30233b5f1 > git rev-list 71d4c282501eaf9ce360a3820e8278d30233b5f1 # timeout=10Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

laserson · 2015-10-06T23:23:44Z

Jenkins, retest this please

laserson · 2015-10-06T23:24:01Z

(it's hard to stay this polite to Jenkins)

AmplabJenkins · 2015-10-06T23:41:45Z

Test PASSed.
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Fixes bigdatagenomics#848.

laserson · 2015-10-06T23:46:11Z

Hallelujah, @fnothaft, think we're good to go.

fnothaft · 2015-10-06T23:48:36Z

Thank you @laserson! I've just merged.

AmplabJenkins · 2015-10-06T23:58:08Z

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laserson mentioned this pull request Oct 6, 2015

Add reference broadcasting to BQSR broadinstitute/gatk#928

Merged

fnothaft reviewed Oct 6, 2015
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fnothaft added this to the 0.18.0 milestone Oct 6, 2015

laserson force-pushed the twobit branch from 3be2dcf to 1f23804 Compare October 6, 2015 21:56

fnothaft reviewed Oct 6, 2015
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laserson force-pushed the twobit branch 2 times, most recently from 1165c0f to 848f24b Compare October 6, 2015 22:08

[ADAM-848] TwoBitFile now support nBlocks and maskBlocks

09f01b3

Fixes bigdatagenomics#848.

laserson force-pushed the twobit branch from c6c9919 to 09f01b3 Compare October 6, 2015 23:45

fnothaft merged commit 09f01b3 into bigdatagenomics:master Oct 6, 2015

laserson deleted the twobit branch October 7, 2015 00:07

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[ADAM-848] TwoBitFile now support nBlocks and maskBlocks #850

[ADAM-848] TwoBitFile now support nBlocks and maskBlocks #850

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[ADAM-848] TwoBitFile now support nBlocks and maskBlocks #850

[ADAM-848] TwoBitFile now support nBlocks and maskBlocks #850

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