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Modified CalculateDepth to get coverage on whole alignment adam files #1010

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@akmorrow13
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akmorrow13 commented Apr 23, 2016

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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/1175/

Build result: FAILURE

GitHub pull request #1010 of commit 4d0510d 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/1010/merge^{commit} # timeout=10 > git branch -a --contains 31569d7f0f819af91bf84f92e278e563c9fc5944 # timeout=10 > git rev-parse remotes/origin/pr/1010/merge^{commit} # timeout=10Checking out Revision 31569d7f0f819af91bf84f92e278e563c9fc5944 (origin/pr/1010/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 31569d7f0f819af91bf84f92e278e563c9fc5944First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Apr 23, 2016

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1175/

Build result: FAILURE

GitHub pull request #1010 of commit 4d0510d 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/1010/merge^{commit} # timeout=10 > git branch -a --contains 31569d7f0f819af91bf84f92e278e563c9fc5944 # timeout=10 > git rev-parse remotes/origin/pr/1010/merge^{commit} # timeout=10Checking out Revision 31569d7f0f819af91bf84f92e278e563c9fc5944 (origin/pr/1010/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 31569d7f0f819af91bf84f92e278e563c9fc5944First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_2.10</artifactId>
<version>${spark.version}</version>

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fnothaft Apr 25, 2016

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Delete here.

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fnothaft Apr 25, 2016

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Delete here.

@@ -440,6 +440,10 @@
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_2.10</artifactId>
</dependency>

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fnothaft Apr 25, 2016

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Add <version>${spark.version}</version> here.

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fnothaft Apr 25, 2016

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Add <version>${spark.version}</version> here.

@@ -53,64 +52,83 @@ class CalculateDepthArgs extends Args4jBase with ParquetArgs {
@Argument(required = true, metaVar = "ADAM", usage = "The Read file to use to calculate depths", index = 0)
val adamInputPath: String = null
@Argument(required = true, metaVar = "VCF", usage = "The VCF containing the sites at which to calculate depths", index = 1)
@Argument(required = true, metaVar = "COVERAGE", usage = "Location to save coverage to parquet file", index = 1)

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fnothaft Apr 25, 2016

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Since -print is an option as well, this should be an option.

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fnothaft Apr 25, 2016

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Since -print is an option as well, this should be an option.

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fnothaft Apr 25, 2016

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Since this is a major modification of CalculateDepth, perhaps we should move this/calculate depth into two separate commands? That would be my preference.

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fnothaft commented Apr 25, 2016

Since this is a major modification of CalculateDepth, perhaps we should move this/calculate depth into two separate commands? That would be my preference.

val sqlContext = new org.apache.spark.sql.SQLContext(sc)
val frequencies = sqlContext.createDataFrame(depths.map(r => Coverage(r._1.referenceName, r._1.start, r._2)))
frequencies.write.parquet(args.outputPath)

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akmorrow13 Apr 25, 2016

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let's save this as a feature

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akmorrow13 Apr 25, 2016

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let's save this as a feature

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fnothaft Jul 6, 2016

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@akmorrow13 I'm going to close this in favor of bigdatagenomics/quinine#14. LMK if you object.

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fnothaft commented Jul 6, 2016

@akmorrow13 I'm going to close this in favor of bigdatagenomics/quinine#14. LMK if you object.

@fnothaft fnothaft closed this Jul 6, 2016

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