Modified CalculateDepth to calcuate coverage from alignment files #1108

akmorrow13 · 2016-08-09T21:50:03Z

Calculates coverage from reads files on command line
Creates CoverageRDD from FeatureRDD

akmorrow13 · 2016-08-09T21:51:48Z

adam-core/src/main/scala/org/bdgenomics/adam/rdd/features/CoverageRDD.scala

+ * @param position Specifies position of coverage
+ * @param count Specifies count of coverage at location
+ */
+case class Coverage(referenceName: String, position: Long, count: Double)


There is already a Coverage class. See here. We do not seem to use this/ these are very different. Is there anything difference I can name my Coverage?

AmplabJenkins · 2016-08-09T21:54:04Z

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GitHub pull request #1108 of commit c773387 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 > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /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 --version # timeout=10 > /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/1108/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 0c70d48af29b2cc5f12301fad0c6323369b7cfa0 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1108/merge^{commit} # timeout=10Checking out Revision 0c70d48af29b2cc5f12301fad0c6323369b7cfa0 (origin/pr/1108/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 0c70d48af29b2cc5f12301fad0c6323369b7cfa0First 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.

akmorrow13 · 2016-08-09T21:54:11Z

adam-core/src/main/scala/org/bdgenomics/adam/rdd/features/CoverageRDD.scala

+ * equal size.
+ *
+ * @param region ReferenceRegion to fetch overlapping coverage from
+ * @param bpPerBin base pairs per bin, number of bases to combine to one bin


This function does a mod for bpPerBin instead of aggregating the bin. However, I couldn't think of how to computing the average size of coverage bins without shuffling. Is this ok?

I have added the option for either aggregation or taking the first element in the bin. There are use cases for both. The use case for no aggregation is visualization, because aggregation provides more information than is required and incurs high overhead. Aggregation of coverage is useful for algorithms that bin coverage by some heuristic.

I don't think you can do the binning without shuffling, so that's OK to me.

Can you document aggregatePerBin? I don't intuitively grok what that parameter does.

AmplabJenkins · 2016-08-09T22:27:24Z

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AmplabJenkins · 2016-08-09T23:36:19Z

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fnothaft · 2016-08-10T04:07:09Z

adam-cli/src/main/scala/org/bdgenomics/adam/cli/Reads2Coverage.scala

+ var inputPath: String = null
+ @Argument(required = true, metaVar = "OUTPUT", usage = "Location to write the coverage data in ADAM/Parquet format", index = 1)
+ var outputPath: String = null
+ @Args4jOption(required = false, name = "-negativeStrands", usage = "Compute coverage for negative strands")


Is there a big use case for stranded coverage info?

Also add "only" to both of these options.

The use case for stranded coverage is for featurization of coverage for DNase in many algorithms. These require separate featurization for negative and positive strands.

AmplabJenkins · 2016-08-10T21:02:19Z

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heuermh · 2016-08-11T03:08:00Z

adam-cli/src/main/scala/org/bdgenomics/adam/cli/Reads2Coverage.scala

+/**
+ * Reads2Coverage (accessible as the command 'coverage' through the CLI) takes two arguments,
+ * an Read file and an output file, and calculates the number of reads from the Read file
+ * at every location in the file. Optional arguments are negativeStrands, and positiveStrands,


argument names should match below

fnothaft · 2016-08-11T04:37:42Z

Hate to be a PITA, but would it be possible to split the deletion of dead code out into a separate commit? LMK if that'd be too much of a hassle.

fnothaft · 2016-08-11T04:45:27Z

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

@@ -757,6 +757,11 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
 FragmentRDD.fromRdd(records.map(fastqRecordConverter.convertFragment))
 }

+ def loadCoverage(filePath: String, minPartitions: Option[Int] = None): CoverageRDD = {


Add scaladoc. Drop unused minPartitions argument?

fnothaft · 2016-08-18T04:46:00Z

adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala

+ CoverageRDD(coverage, sequences).collapse
+ else CoverageRDD(coverage, sequences)
+
+ coverage.unpersist()


You don't want to unpersist coverage. You'd want to unpersist covCounts from https://github.com/bigdatagenomics/adam/pull/1108/files#r75248157. Calling unpersist on coverage should cause everything done to the CoverageRDD returned by this method to throw an exception...

fnothaft · 2016-08-18T04:47:23Z

Dropped a variety of nits inline; all in all looks good!

AmplabJenkins · 2016-08-18T23:25:39Z

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[...truncated 24 lines...]Triggering ADAM-prb ? 2.3.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.3.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result SUCCESSADAM-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 ? 2.3.0,2.10,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

akmorrow13 · 2016-08-18T23:38:46Z

Jenkins, test this please.

AmplabJenkins · 2016-08-18T23:49:13Z

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AmplabJenkins · 2016-08-19T00:11:21Z

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[...truncated 24 lines...]Triggering ADAM-prb ? 2.3.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.3.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result SUCCESSADAM-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 ? 2.3.0,2.10,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
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AmplabJenkins · 2016-08-19T00:34:10Z

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[...truncated 24 lines...]Triggering ADAM-prb ? 2.3.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.3.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result SUCCESSADAM-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 ? 2.3.0,2.10,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

akmorrow13 · 2016-08-19T02:12:42Z

Jenkins, retest this please.

AmplabJenkins · 2016-08-19T02:37:28Z

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fnothaft · 2016-08-23T16:21:49Z

Thanks for merging my PR against this PR, @akmorrow13! Can you remove the merge commit b13eee5?

AmplabJenkins · 2016-08-23T16:33:57Z

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GitHub pull request #1108 of commit b13eee5 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 > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /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 --version # timeout=10 > /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/1108/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 4081f7276c8fe83b78333293c591043d0725bfb7 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1108/merge^{commit} # timeout=10Checking out Revision 4081f7276c8fe83b78333293c591043d0725bfb7 (origin/pr/1108/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 4081f7276c8fe83b78333293c591043d0725bfb7 > /home/jenkins/git2/bin/git rev-list 3ec3f47209cbea6321e44d764058d0a90331789c # timeout=10Triggering 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'
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AmplabJenkins · 2016-08-23T17:19:04Z

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[...truncated 24 lines...]Triggering ADAM-prb ? 2.3.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.3.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result SUCCESSADAM-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 ? 2.3.0,2.10,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2016-08-23T17:41:02Z

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[...truncated 24 lines...]Triggering ADAM-prb ? 2.3.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.3.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result SUCCESSADAM-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 ? 2.3.0,2.10,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2016-08-24T18:08:26Z

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[...truncated 24 lines...]Triggering ADAM-prb ? 2.3.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.3.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2016-08-25T17:17:29Z

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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1424/

Build result: FAILURE

[...truncated 24 lines...]Triggering ADAM-prb ? 2.3.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.3.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result SUCCESSADAM-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 ? 2.3.0,2.10,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

heuermh · 2016-08-25T23:25:14Z

Closing in favor of #1128

akmorrow13 reviewed Aug 9, 2016
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akmorrow13 force-pushed the coverage branch from c773387 to 1624df6 Compare August 9, 2016 22:01

akmorrow13 force-pushed the coverage branch from 1624df6 to 9534624 Compare August 9, 2016 23:09

fnothaft reviewed Aug 10, 2016
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akmorrow13 force-pushed the coverage branch from 9534624 to 0ce5218 Compare August 10, 2016 20:34

heuermh reviewed Aug 11, 2016
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fnothaft reviewed Aug 11, 2016
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fnothaft reviewed Aug 18, 2016
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akmorrow13 force-pushed the coverage branch 2 times, most recently from 05ff4bd to f15afe5 Compare August 18, 2016 23:15

akmorrow13 force-pushed the coverage branch 2 times, most recently from a151cf6 to a5ced0f Compare August 18, 2016 23:37

fnothaft mentioned this pull request Aug 23, 2016

Remove PairingRDD #1122

Closed

akmorrow13 force-pushed the coverage branch from 9650140 to 6d54630 Compare August 23, 2016 17:12

akmorrow13 force-pushed the coverage branch from 6d54630 to c9e5f79 Compare August 24, 2016 17:42

fnothaft mentioned this pull request Aug 25, 2016

PR #1108 with issue #1122 #1128

Merged

Added support for coverage calculation from alignment files

ed30926

akmorrow13 force-pushed the coverage branch from c9e5f79 to ed30926 Compare August 25, 2016 16:58

heuermh closed this Aug 25, 2016

akmorrow13 deleted the coverage branch November 1, 2016 19:30

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Modified CalculateDepth to calcuate coverage from alignment files #1108

Modified CalculateDepth to calcuate coverage from alignment files #1108

akmorrow13 commented Aug 9, 2016

akmorrow13 Aug 9, 2016

AmplabJenkins commented Aug 9, 2016

akmorrow13 Aug 9, 2016

akmorrow13 Aug 9, 2016

fnothaft Aug 10, 2016

fnothaft Aug 10, 2016

AmplabJenkins commented Aug 9, 2016

AmplabJenkins commented Aug 9, 2016

fnothaft Aug 10, 2016

fnothaft Aug 10, 2016

akmorrow13 Aug 10, 2016

AmplabJenkins commented Aug 10, 2016

heuermh Aug 11, 2016

fnothaft commented Aug 11, 2016

fnothaft Aug 11, 2016

fnothaft Aug 18, 2016

fnothaft commented Aug 18, 2016

AmplabJenkins commented Aug 18, 2016

akmorrow13 commented Aug 18, 2016

AmplabJenkins commented Aug 18, 2016

AmplabJenkins commented Aug 19, 2016

AmplabJenkins commented Aug 19, 2016

akmorrow13 commented Aug 19, 2016

AmplabJenkins commented Aug 19, 2016

fnothaft commented Aug 23, 2016

AmplabJenkins commented Aug 23, 2016

AmplabJenkins commented Aug 23, 2016

AmplabJenkins commented Aug 23, 2016

AmplabJenkins commented Aug 24, 2016

AmplabJenkins commented Aug 25, 2016

heuermh commented Aug 25, 2016

Modified CalculateDepth to calcuate coverage from alignment files #1108

Modified CalculateDepth to calcuate coverage from alignment files #1108

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akmorrow13 commented Aug 9, 2016

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Build result: FAILURE

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AmplabJenkins commented Aug 9, 2016

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fnothaft commented Aug 18, 2016

AmplabJenkins commented Aug 18, 2016

Build result: FAILURE

akmorrow13 commented Aug 18, 2016

AmplabJenkins commented Aug 18, 2016

AmplabJenkins commented Aug 19, 2016

Build result: FAILURE

AmplabJenkins commented Aug 19, 2016

Build result: FAILURE

akmorrow13 commented Aug 19, 2016

AmplabJenkins commented Aug 19, 2016

fnothaft commented Aug 23, 2016

AmplabJenkins commented Aug 23, 2016

Build result: FAILURE

AmplabJenkins commented Aug 23, 2016

Build result: FAILURE

AmplabJenkins commented Aug 23, 2016

Build result: FAILURE

AmplabJenkins commented Aug 24, 2016

Build result: FAILURE

AmplabJenkins commented Aug 25, 2016

Build result: FAILURE

heuermh commented Aug 25, 2016