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[ADAM-462] Coverage region calculation #482

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merged 1 commit into from Dec 2, 2014

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@tdanford
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tdanford commented Nov 16, 2014

This commit includes an new class, Coverage, which contains methods for
calculating coverage RDDs from RDDs of Region values.

Also included is a helper class, the PairingRDD class, which calculates
simple 'sliding' and 'pair' methods on sorted RDDs using the
"zipWithIndex trick."

(Joint work with Carl Yeksigian, and fixes #462)

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GitHub pull request #482 of commit 61563f3 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/482/merge^{commit} # timeout=10Checking out Revision 3ff4655 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 3ff4655 > git rev-list f211b54 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILURE
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GitHub pull request #482 of commit 61563f3 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/482/merge^{commit} # timeout=10Checking out Revision 3ff4655 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 3ff4655 > git rev-list f211b54 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILURE
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/**
* A base is 'covered' by a region set if any region in the set contains the base itself.
*
* The 'coverage regions' of a region set are the unique, disjoint, non-adjacent,

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fnothaft Nov 18, 2014

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Why is it non-adjacent? Also, how does minimal come in?

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fnothaft Nov 18, 2014

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Why is it non-adjacent? Also, how does minimal come in?

require(window > 0)
type Region = ReferenceRegion

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fnothaft Nov 18, 2014

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Is there a reason to type this?

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fnothaft Nov 18, 2014

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Is there a reason to type this?

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tdanford Nov 18, 2014

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I got tired of writing out ReferenceRegion the whole time.

Also, it used to be a type parameter.

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tdanford Nov 18, 2014

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I got tired of writing out ReferenceRegion the whole time.

Also, it used to be a type parameter.

* @param width The 'width' of the sliding window to calculate
* @return An RDD of the sliding window values
*/
def sliding(width: Int): RDD[Seq[T]] = {

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What's the speed difference between flatMapping and then doing a groupBy vs. doing a join?

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What's the speed difference between flatMapping and then doing a groupBy vs. doing a join?

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tdanford Nov 25, 2014

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Frank, I'm confused by your question here. Which flatMap and groupBy are you referring to?

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tdanford Nov 25, 2014

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Frank, I'm confused by your question here. Which flatMap and groupBy are you referring to?

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L71 is a fold that performs n joins on RDDs, no? My question is whether it'd be more efficient to do a flatMap (well, actually a reduce(_ ++ _) since they're RDDs), followed by a groupByKey, instead of doing n joins.

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L71 is a fold that performs n joins on RDDs, no? My question is whether it'd be more efficient to do a flatMap (well, actually a reduce(_ ++ _) since they're RDDs), followed by a groupByKey, instead of doing n joins.

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tdanford Nov 28, 2014

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Frank, I've changed the implementation in the latest commit, let me know if it does (or doesn't) reflect what you were suggesting.

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tdanford Nov 28, 2014

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Frank, I've changed the implementation in the latest commit, let me know if it does (or doesn't) reflect what you were suggesting.

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GitHub pull request #482 of commit 3c7269b 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/482/merge^{commit} # timeout=10Checking out Revision 694eece (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 694eece > git rev-list f211b54 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILURE
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GitHub pull request #482 of commit 3c7269b 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/482/merge^{commit} # timeout=10Checking out Revision 694eece (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 694eece > git rev-list f211b54 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILURE
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So, I'm not entirely clear here. What is a coverage region? Is that supposed to refer to a contiguous region that is covered?

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fnothaft commented Nov 18, 2014

So, I'm not entirely clear here. What is a coverage region? Is that supposed to refer to a contiguous region that is covered?

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Yes. But also a minimal set of such regions -- by which I mean, no two coverage regions overlap or are adjacent (i.e. have zero space between them, because then they could be merged into a single contiguous region.)

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tdanford commented Nov 18, 2014

Yes. But also a minimal set of such regions -- by which I mean, no two coverage regions overlap or are adjacent (i.e. have zero space between them, because then they could be merged into a single contiguous region.)

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This appears to be more Jenkins errors, right @fnothaft?

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tdanford commented Nov 19, 2014

This appears to be more Jenkins errors, right @fnothaft?

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@tdanford Yep...

Jenkins, retest this please.

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fnothaft commented Nov 19, 2014

@tdanford Yep...

Jenkins, retest this please.

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GitHub pull request #482 of commit 2758ad4 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/482/merge^{commit} # timeout=10Checking out Revision dac2cfe (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f dac2cfe > git rev-list a111506 # 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 FAILUREADAM-prb » 1.0.4,centos completed with result FAILURE
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GitHub pull request #482 of commit 2758ad4 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/482/merge^{commit} # timeout=10Checking out Revision dac2cfe (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f dac2cfe > git rev-list a111506 # 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 FAILUREADAM-prb » 1.0.4,centos completed with result FAILURE
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jenkins, test this please

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shaneknapp commented Nov 25, 2014

jenkins, test this please

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GitHub pull request #482 of commit bcc0dec 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/482/merge^{commit} # timeout=10Checking out Revision 050a31c (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 050a31c > git rev-list 9c15ef40777b94d6598b258d478db7d134b25270 # 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
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GitHub pull request #482 of commit bcc0dec 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/482/merge^{commit} # timeout=10Checking out Revision 050a31c (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 050a31c > git rev-list 9c15ef40777b94d6598b258d478db7d134b25270 # 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
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@fnothaft I think I've addressed all your comments -- let me know if I missed anything? Otherwise, if this builds correctly (and unless anyone else would like to review it), I think it's ready for a rebase-and-merge.

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tdanford commented Nov 28, 2014

@fnothaft I think I've addressed all your comments -- let me know if I missed anything? Otherwise, if this builds correctly (and unless anyone else would like to review it), I think it's ready for a rebase-and-merge.

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GitHub pull request #482 of commit fe580eb 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/482/merge^{commit} # timeout=10Checking out Revision 7402be7 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 7402be7 > git rev-list 5a0da27709bd2cf28bafa0d2f5e88e429184f6dd # 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
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GitHub pull request #482 of commit fe580eb 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/482/merge^{commit} # timeout=10Checking out Revision 7402be7 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 7402be7 > git rev-list 5a0da27709bd2cf28bafa0d2f5e88e429184f6dd # 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
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Jenkins retest this please.

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tdanford commented Nov 28, 2014

Jenkins retest this please.

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Ping @fnothaft

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tdanford commented Dec 2, 2014

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@tdanford thanks, this looks good now. Can you rebase and I'll merge?

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fnothaft commented Dec 2, 2014

@tdanford thanks, this looks good now. Can you rebase and I'll merge?

[ADAM-462] Coverage region calculation
This commit includes an new class, Coverage, which contains methods for
calculating coverage RDDs from RDDs of Region values.

Also included is a helper class, the PairingRDD class, which calculates
simple 'sliding' and 'pair' methods on sorted RDDs using the
"zipWithIndex trick."

(Joint work with Carl Yeksigian.)
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@fnothaft I've rebased and squashed, if the tests pass, I think it's ready.

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tdanford commented Dec 2, 2014

@fnothaft I've rebased and squashed, if the tests pass, I think it's ready.

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GitHub pull request #482 of commit bcacc57 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/482/merge^{commit} # timeout=10Checking out Revision 6fa082ec29f5a97881474d5b418819f8f31677d6 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 6fa082ec29f5a97881474d5b418819f8f31677d6 > git rev-list ce6774b # 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
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/477/

Build result: FAILURE

GitHub pull request #482 of commit bcacc57 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/482/merge^{commit} # timeout=10Checking out Revision 6fa082ec29f5a97881474d5b418819f8f31677d6 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 6fa082ec29f5a97881474d5b418819f8f31677d6 > git rev-list ce6774b # 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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Jenkins, retest this please.

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fnothaft commented Dec 2, 2014

Jenkins, retest this please.

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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/478/
Test PASSed.

AmplabJenkins commented Dec 2, 2014

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/478/
Test PASSed.

fnothaft added a commit that referenced this pull request Dec 2, 2014

Merge pull request #482 from tdanford/coverage-regions
[ADAM-462] Coverage region calculation

@fnothaft fnothaft merged commit db7c1dd into bigdatagenomics:master Dec 2, 2014

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Merged! Thanks @tdanford.

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fnothaft commented Dec 2, 2014

Merged! Thanks @tdanford.

@tdanford tdanford deleted the tdanford:coverage-regions branch Dec 2, 2014

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