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[ADAM-1224] Replace BroadcastRegionJoin with tree based algo. #1234

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@fnothaft
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fnothaft commented Nov 1, 2016

WIP towards #1224. To be done:

  • Add more tests for outer joins
  • Fix serialization stuff (note disconnected ForestSerializer)

The custom serializer is necessary because Kryo does not serialize large arrays properly, which is... concerning.

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AmplabJenkins commented Nov 1, 2016

Test PASSed.
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AmplabJenkins commented Nov 3, 2016

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jpdna commented Nov 3, 2016

Is this ready for someone else to test/review or do you have further work to do @fnothaft ? Ping when you do want review.

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fnothaft commented Nov 3, 2016

@jpdna I need to write some more unit tests, but otherwise the core of the code is ready for review!

/**
* Companion object for building a forest from an RDD.
*/
private[adam] object Forest extends Serializable {

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akmorrow13 Nov 8, 2016

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If we are using the implementation for IntervalRDD, we would most likely be moving Forest and ForestSerializer to utils. Is there anything else that should be moved to utils?

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I think that is all.

@fnothaft fnothaft added this to the 0.21.0 milestone Nov 8, 2016
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jpdna commented Nov 11, 2016

I notice that in the overlaps functions of referenceRegion called in binarySearch that there is a requirement that orientation be the same in order to return true:

At first glance, I'm wondering if this is a problem, for example if joining a deletion or other feature expressed on the positive strand against a gene or transcript where Orientation=Strand.REVERSE

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jpdna commented Nov 11, 2016

Also, I have small itch of concern ( which I haven't tested yet) that there could a scenario where
expand
https://github.com/bigdatagenomics/adam/pull/1234/files#diff-7dca5f64826de300ea13b67c5ce39687R94
stops searching further into the sorted referenceRegion broadcast array because the next referenceRegion it finds doesn't overlap, but further upstream or downstream in the array there is larger referenceRegion feature that does overlap.

Like


query                                         ---

brod_array                        --       ----------   --
                            --------------------------------------------------

this may well be just fine, just wanted to note it.
They broadcast array is sorted by start position of ReferenceRegions correct?

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jpdna commented Nov 14, 2016

ping wrt to my two comments above

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fnothaft commented Nov 26, 2016

I've upgraded this on top of bigdatagenomics/utils#94 in the last commit (and rebased) but it fails one unit test due to some serializer funniness. I'm going to make a cleanup pass on utils/#94 tomorrow to fix this.

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Test FAILed.
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Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git -c core.askpass=true 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/1234/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 33d5bfb # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1234/merge^{commit} # timeout=10Checking out Revision 33d5bfb (origin/pr/1234/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 33d5bfb81f2cb680215dd109f280fd676a06ee6eFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@fnothaft fnothaft force-pushed the fnothaft:issues/1224-true-broadcast-join branch from e5af388 to 4baec6c Nov 29, 2016
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Test FAILed.
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Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git -c core.askpass=true 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/1234/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 029c27c3f78304082d4d8c8f999d29685122f6da # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1234/merge^{commit} # timeout=10Checking out Revision 029c27c3f78304082d4d8c8f999d29685122f6da (origin/pr/1234/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 029c27c3f78304082d4d8c8f999d29685122f6daFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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fnothaft commented Nov 29, 2016

Jenkins, retest this please.

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Test FAILed.
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Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git -c core.askpass=true 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/1234/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 029c27c3f78304082d4d8c8f999d29685122f6da # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1234/merge^{commit} # timeout=10Checking out Revision 029c27c3f78304082d4d8c8f999d29685122f6da (origin/pr/1234/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 029c27c3f78304082d4d8c8f999d29685122f6daFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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fnothaft commented Nov 29, 2016

Jenkins, test this please.

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Test FAILed.
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Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git -c core.askpass=true 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/1234/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 029c27c3f78304082d4d8c8f999d29685122f6da # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1234/merge^{commit} # timeout=10Checking out Revision 029c27c3f78304082d4d8c8f999d29685122f6da (origin/pr/1234/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 029c27c3f78304082d4d8c8f999d29685122f6daFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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fnothaft commented Nov 29, 2016

Jenkins, retest this please.

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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/1645/

Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git -c core.askpass=true 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/1234/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 029c27c3f78304082d4d8c8f999d29685122f6da # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1234/merge^{commit} # timeout=10Checking out Revision 029c27c3f78304082d4d8c8f999d29685122f6da (origin/pr/1234/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 029c27c3f78304082d4d8c8f999d29685122f6daFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@fnothaft fnothaft force-pushed the fnothaft:issues/1224-true-broadcast-join branch from 4baec6c to 6ce69dd Nov 29, 2016
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Test FAILed.
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Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git -c core.askpass=true 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/1234/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 4692c68e1b45b71e2ba65f50f738393a9cd4c23e # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1234/merge^{commit} # timeout=10Checking out Revision 4692c68e1b45b71e2ba65f50f738393a9cd4c23e (origin/pr/1234/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 4692c68e1b45b71e2ba65f50f738393a9cd4c23eFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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fnothaft commented Nov 29, 2016

Jenkins, retest this please.

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Test PASSed.
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Test PASSed.

@fnothaft fnothaft force-pushed the fnothaft:issues/1224-true-broadcast-join branch from 6ce69dd to 8dba8e7 Dec 1, 2016
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fnothaft commented Dec 1, 2016

This is squashed down and good to go!

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Test FAILed.
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Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git -c core.askpass=true 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/1234/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains f3bf2e7cccca2f4a1e034fd0d8569235c8c16172 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1234/merge^{commit} # timeout=10Checking out Revision f3bf2e7cccca2f4a1e034fd0d8569235c8c16172 (origin/pr/1234/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f f3bf2e7cccca2f4a1e034fd0d8569235c8c16172First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@fnothaft fnothaft force-pushed the fnothaft:issues/1224-true-broadcast-join branch from 8dba8e7 to 4136e9a Dec 1, 2016
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Test PASSed.
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Test PASSed.

@@ -2,7 +2,7 @@

set +x

find . -name "pom.xml" -exec sed -e "s/2.10.6/2.11.8/g" -e "s/2.10/2.11/g" -i.2.11.bak '{}' \;
find . -name "pom.xml" -exec sed -e "s/2.10.6/2.11.8/g" -e "/bdg-utils.version/!s/2.10/2.11/g" -i.2.11.bak '{}' \;

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heuermh Dec 7, 2016

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What is this for? Do we need something similar in move_to_scala_2.10.sh?

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fnothaft Dec 7, 2016

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The utils version bumps to 0.2.10 in this PR. If you don't filter out that line when running the sed replacements, then it changes the utils version to 0.2.11. This doesn't happen going 2.11->2.10, since the replacement is different.

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I see, good catch :)

fnothaft added 2 commits Nov 1, 2016
Resolves #1224. Adds and fixes docs. Updating for utils/#94 and bumps to
utils 0.2.10 release.
@fnothaft fnothaft force-pushed the fnothaft:issues/1224-true-broadcast-join branch from 4136e9a to bf136e5 Dec 7, 2016
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fnothaft commented Dec 7, 2016

Rebased and resolved conflicts.

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heuermh approved these changes Dec 7, 2016
@heuermh heuermh merged commit 4ae84e4 into bigdatagenomics:master Dec 7, 2016
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heuermh commented Dec 7, 2016

Thank you, @fnothaft

@fnothaft fnothaft deleted the fnothaft:issues/1224-true-broadcast-join branch Dec 7, 2016
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