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[CANNOLI-104] Provide functions for use in cannoli-shell or notebooks. #69

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merged 1 commit into from Feb 27, 2018

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@heuermh heuermh commented Sep 12, 2017

Fixes #104.

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@heuermh heuermh commented Nov 8, 2017

Ping @akmorrow13 for review.

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/**
* Bedtools command arguments.
*/

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akmorrow13 Nov 8, 2017

It might be good to put a more detailed explanation of why we have BedtoolsFnArgs as well as BedtoolsArgs

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@heuermh heuermh force-pushed the heuermh:cannoli-fn branch from b251123 to 2037a33 Feb 8, 2018
@heuermh heuermh added this to the 0.2.0 milestone Feb 8, 2018
@heuermh heuermh self-assigned this Feb 8, 2018
@heuermh heuermh changed the title Adding bedtools function. [CANNOLI-104] Provide functions for use in cannoli-shell or notebooks. Feb 8, 2018
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@heuermh heuermh commented Feb 8, 2018

Rebased with BedtoolsFn as an example for review, will continue with the other commands.

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@coveralls coveralls commented Feb 8, 2018

Coverage Status

Coverage decreased (-2.04%) to 23.455% when pulling f7228a4 on heuermh:cannoli-fn into 23a4585 on bigdatagenomics:master.

@heuermh heuermh force-pushed the heuermh:cannoli-fn branch from 2037a33 to f4c14da Feb 8, 2018

val sample = args.sample

val output: AlignmentRecordRDD = new BwaFn(args, sc).apply(input)

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heuermh Feb 8, 2018
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@fnothaft I wasn't sure if the next line (.replaceRecordGroups) should be inside the BwaFn function or should remain here in the command line wrapper.

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@heuermh heuermh commented Feb 8, 2018

For example, this is what BedtoolsFn looks like in cannoli-shell

$ ./bin/cannoli-shell 

Welcome to
      ____              __
     / __/__  ___ _____/ /__
    _\ \/ _ \/ _ `/ __/  '_/
   /___/ .__/\_,_/_/ /_/\_\   version 2.2.1
      /_/
         
Using Scala version 2.11.8 (Java HotSpot(TM) 64-Bit Server VM, Java 1.8.0_66)
Type in expressions to have them evaluated.
Type :help for more information.

scala> import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.adam.rdd.ADAMContext._

scala> val features = sc.loadFeatures("../adam/adam-core/src/test/resources/dvl1.200.bed")
features: org.bdgenomics.adam.rdd.feature.FeatureRDD = RDDBoundFeatureRDD with 0 reference sequences

scala> features.rdd.count()
res0: Long = 197                                                                

scala> import org.bdgenomics.cannoli.cli._
import org.bdgenomics.cannoli.cli._

scala> val args = new BedtoolsFnArgs()
args: org.bdgenomics.cannoli.cli.BedtoolsFnArgs = org.bdgenomics.cannoli.cli.BedtoolsFnArgs@2a5c6b76

scala> args.b = "region.bed"
args.b: String = region.bed

scala> val intersection = new BedtoolsFn(args).apply(features)
intersection: org.bdgenomics.adam.rdd.feature.FeatureRDD = RDDBoundFeatureRDD with 0 reference sequences

scala> intersection.rdd.count()
res1: Long = 1

scala> intersection.rdd.first
res2: org.bdgenomics.formats.avro.Feature = {"featureId": null, "name": "106668", ...
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Build result: FAILURE

GitHub pull request #69 of commit 0c9c99a automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-03 (centos spark-test) in workspace /home/jenkins/workspace/cannoli-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/cannoli.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/cannoli-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/cannoli.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/cannoli.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/cannoli.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/cannoli.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/cannoli.git > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/cannoli.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/69/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 6f3cc02 # timeout=10Checking out Revision 6f3cc02 (origin/pr/69/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 6f3cc0252c9ced11ca3ff96ac2777dcbdf738834First time build. Skipping changelog.Triggering cannoli-prb ? 2.7.3,2.11,2.2.1,centoscannoli-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@heuermh heuermh force-pushed the heuermh:cannoli-fn branch from 0c9c99a to 34348ee Feb 9, 2018
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@heuermh heuermh force-pushed the heuermh:cannoli-fn branch from 34348ee to f7228a4 Feb 20, 2018
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@heuermh heuermh merged commit 0ab8543 into bigdatagenomics:master Feb 27, 2018
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@heuermh heuermh deleted the heuermh:cannoli-fn branch Feb 27, 2018
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