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[ADAM-710] Add saveAs methods for feature formats GTF, BED, IntervalList, and NarrowPeak #998

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heuermh commented Apr 13, 2016

Fixes #710.

Pushing this early for review.

Still todo is writing IntervalList header and -single file support, if that might be desirable. Currently this uses Spark saveAsTextFile which writes to as many part-00... text files as there are partitions.

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GitHub pull request #998 of commit 72f238f 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/998/merge^{commit} # timeout=10 > git branch -a --contains 385dbc23bcb4b849c4303829347615c78cacdb0e # timeout=10 > git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 385dbc23bcb4b849c4303829347615c78cacdb0e (origin/pr/998/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 385dbc23bcb4b849c4303829347615c78cacdb0eFirst 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'
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GitHub pull request #998 of commit 72f238f 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/998/merge^{commit} # timeout=10 > git branch -a --contains 385dbc23bcb4b849c4303829347615c78cacdb0e # timeout=10 > git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 385dbc23bcb4b849c4303829347615c78cacdb0e (origin/pr/998/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 385dbc23bcb4b849c4303829347615c78cacdb0eFirst 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'
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GitHub pull request #998 of commit 3630a26 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/998/merge^{commit} # timeout=10 > git branch -a --contains 7d86cfe3d4f8646f59969530f775bc58976348b5 # timeout=10 > git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 7d86cfe3d4f8646f59969530f775bc58976348b5 (origin/pr/998/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 7d86cfe3d4f8646f59969530f775bc58976348b5First 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'
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GitHub pull request #998 of commit 3630a26 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/998/merge^{commit} # timeout=10 > git branch -a --contains 7d86cfe3d4f8646f59969530f775bc58976348b5 # timeout=10 > git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 7d86cfe3d4f8646f59969530f775bc58976348b5 (origin/pr/998/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 7d86cfe3d4f8646f59969530f775bc58976348b5First 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'
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[...truncated 24 lines...]Triggering ADAM-prb ? 2.6.0,2.10,1.3.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.0,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.5.2,centosADAM-prb ? 2.6.0,2.11,1.6.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.5.2,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
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[...truncated 24 lines...]Triggering ADAM-prb ? 2.6.0,2.10,1.3.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.0,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.5.2,centosADAM-prb ? 2.6.0,2.11,1.6.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.5.2,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
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heuermh commented Apr 20, 2016

@heuermh heuermh added the needs work label Apr 21, 2016

@heuermh heuermh changed the title from Add saveAs methods for feature formats GTF, BED, IntervalList, and NarrowPeak to [ADAM-710] Add saveAs methods for feature formats GTF, BED, IntervalList, and NarrowPeak Apr 21, 2016

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@tdanford bump for feedback, see last comment

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heuermh commented May 18, 2016

@tdanford bump for feedback, see last comment

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@heuermh what needs work on this PR? Do you think we can get this in to 0.20.0 (end of month)?

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fnothaft commented May 18, 2016

@heuermh what needs work on this PR? Do you think we can get this in to 0.20.0 (end of month)?

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The four items in the comment above that need review and single-file SAM/BAM-style header support for IntervalList similar to that described in #1009.

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heuermh commented May 18, 2016

The four items in the comment above that need review and single-file SAM/BAM-style header support for IntervalList similar to that described in #1009.

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OK. I'll get going on the review.

single-file SAM/BAM-style header support for IntervalList similar to that described in #1009.

What does the IntervalList header look like? I'll work on #1009 and we can then slot this on top.

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fnothaft commented May 18, 2016

OK. I'll get going on the review.

single-file SAM/BAM-style header support for IntervalList similar to that described in #1009.

What does the IntervalList header look like? I'll work on #1009 and we can then slot this on top.

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What does the IntervalList header look like?

"The file format is relatively simple and reflects the SAM alignment format to a degree. A SAM style header must be present in the file which lists the sequence records against which the intervals are described."

https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/util/IntervalList.html

Thus we might be able to reuse the SAM header stuff directly; the current IntervalList parsing code does not. You had mentioned refactoring the SAM/BAM header code although maybe not as part of #1009; I can pick this up based on what you do there.

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heuermh commented May 18, 2016

What does the IntervalList header look like?

"The file format is relatively simple and reflects the SAM alignment format to a degree. A SAM style header must be present in the file which lists the sequence records against which the intervals are described."

https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/util/IntervalList.html

Thus we might be able to reuse the SAM header stuff directly; the current IntervalList parsing code does not. You had mentioned refactoring the SAM/BAM header code although maybe not as part of #1009; I can pick this up based on what you do there.

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Thus we might be able to reuse the SAM header stuff directly; the current IntervalList parsing code does not. You had mentioned refactoring the SAM/BAM header code although maybe not as part of #1009; I can pick this up based on what you do there.

I would prefer using the SAM header code to rolling our own.

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fnothaft commented May 18, 2016

Thus we might be able to reuse the SAM header stuff directly; the current IntervalList parsing code does not. You had mentioned refactoring the SAM/BAM header code although maybe not as part of #1009; I can pick this up based on what you do there.

I would prefer using the SAM header code to rolling our own.

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GitHub pull request #998 of commit 35af436 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 95b97512b3abd38a07c7f6fc97460bea315cb338 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 95b97512b3abd38a07c7f6fc97460bea315cb338 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 95b97512b3abd38a07c7f6fc97460bea315cb338First 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'
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GitHub pull request #998 of commit 35af436 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 95b97512b3abd38a07c7f6fc97460bea315cb338 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 95b97512b3abd38a07c7f6fc97460bea315cb338 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 95b97512b3abd38a07c7f6fc97460bea315cb338First 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'
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Show outdated Hide outdated ...core/src/main/scala/org/bdgenomics/adam/rdd/features/FeatureParser.scala
@@ -118,7 +122,11 @@ class GTFParser extends FeatureParser {
_id.foreach(f.setFeatureId)
_parentId.foreach(parentId => f.setParentIds(List[String](parentId)))
f.setAttributes(attrs)
if (frame != ".") {
f.setAttributes(collection.mutable.Map(attrs.toSeq: _*) += ("frame" -> frame))

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collection.mutable.Map(attrs.toSeq: _*) += ("frame" -> frame) to attrs.map(v -> ("frame", v)).toMap)?

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collection.mutable.Map(attrs.toSeq: _*) += ("frame" -> frame) to attrs.map(v -> ("frame", v)).toMap)?

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Also, could we get some docs here? What's this conditional for? It looks like we're special casing some formatting thing. Why's that? Etc.

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Also, could we get some docs here? What's this conditional for? It looks like we're special casing some formatting thing. Why's that? Etc.

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Yeah I don't like it, I will propose adding frame as an attribute to Feature in an upcoming pull request.

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Yeah I don't like it, I will propose adding frame as an attribute to Feature in an upcoming pull request.

Show outdated Hide outdated ...core/src/main/scala/org/bdgenomics/adam/rdd/features/FeatureParser.scala
@@ -96,6 +96,10 @@ class GTFParser extends FeatureParser {
.setFeatureType(feature)
.setSource(source)
if (score != ".") {

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Ditto here RE: adding docs for special case code.

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Ditto here RE: adding docs for special case code.

Show outdated Hide outdated ...core/src/main/scala/org/bdgenomics/adam/rdd/features/FeatureParser.scala
@@ -177,6 +185,7 @@ class IntervalListParser extends Serializable {
Feature.newBuilder()
.setContig(Contig.newBuilder().setContigName(fields(0)).build())
.setStart(fields(1).toLong - 1)
// todo: IntervalList ranges are closed, is this correct?

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This is correct. Drop todo but keep comment as documentation? E.g., // NOTE: IntervalList ranges are closed

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This is correct. Drop todo but keep comment as documentation? E.g., // NOTE: IntervalList ranges are closed

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If IntervalList intervals are 1-based and closed, shouldn't the next line be

.setEnd(fields(2).toLong)

E.g. [7-9] in IntervalList should be [6-9) in our 0-based, closed open system.

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If IntervalList intervals are 1-based and closed, shouldn't the next line be

.setEnd(fields(2).toLong)

E.g. [7-9] in IntervalList should be [6-9) in our 0-based, closed open system.

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Agreed, my correct was RE: the comment.

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Agreed, my correct was RE: the comment.

Show outdated Hide outdated ...core/src/main/scala/org/bdgenomics/adam/rdd/features/FeatureParser.scala
@@ -196,8 +205,16 @@ class IntervalListParser extends Serializable {
class BEDParser extends FeatureParser {
def isHeader(line: String): Boolean = {
return line.startsWith("#") || line.startsWith("browser") || line.startsWith("track")

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Nit: Drop return

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Nit: Drop return

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heuermh May 19, 2016

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What, you want my Scala not to look like Java? :)

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What, you want my Scala not to look like Java? :)

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Show outdated Hide outdated ...core/src/main/scala/org/bdgenomics/adam/rdd/features/FeatureParser.scala
override def parse(line: String): Seq[Feature] = {
if (isHeader(line)) {
return Seq()

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Ditto here. I'd rather refactor the function so that we eliminate all return statements.

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Ditto here. I'd rather refactor the function so that we eliminate all return statements.

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fnothaft Jun 14, 2016

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Ping.

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here I find it better to short circuit return than to put the whole method in an if block

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here I find it better to short circuit return than to put the whole method in an if block

Show outdated Hide outdated ...core/src/main/scala/org/bdgenomics/adam/rdd/features/FeatureParser.scala
@@ -230,22 +247,22 @@ class BEDParser extends FeatureParser {
})
}
val attributes = new ArrayBuffer[(String, String)]()
if (fields.length > 6) {
if (fields.length > 6 && fields(6) != ".") {

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It seems like there's a lot of repeated code here. Could we refactor? E.g.:

def attrExists(attrIdx: Int, attr: String) {
  if (fields.length > attrIdx && fields(attrIdx) != ".") {
    attributes += ("attr" -> fields(attrIdx)
  }
}

attrExists(6, "thickStart")
attrExists(7, "thickEnd")
...
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It seems like there's a lot of repeated code here. Could we refactor? E.g.:

def attrExists(attrIdx: Int, attr: String) {
  if (fields.length > attrIdx && fields(attrIdx) != ".") {
    attributes += ("attr" -> fields(attrIdx)
  }
}

attrExists(6, "thickStart")
attrExists(7, "thickEnd")
...
Show outdated Hide outdated ...rc/main/scala/org/bdgenomics/adam/rdd/features/FeatureRDDFunctions.scala
Joiner.on('\t').join(chrom, start, end, name, score, strand)
} else {
// write BED12 format
val thickStart = feature.getAttributes.getOrElse("thickStart", ".")

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I would factor this out --> feature.getAttributes.getOrElse(attr, ".") to:

def getAttr(attr: String): String = {
  feature.getAttributes.getOrElse(attr, ".")
}

val thickStart = getAttr("thickStart")
...
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I would factor this out --> feature.getAttributes.getOrElse(attr, ".") to:

def getAttr(attr: String): String = {
  feature.getAttributes.getOrElse(attr, ".")
}

val thickStart = getAttr("thickStart")
...
Show outdated Hide outdated ...rc/main/scala/org/bdgenomics/adam/rdd/features/FeatureRDDFunctions.scala
case Strand.Reverse => "-"
case Strand.Independent => "."
}
val signalValue = feature.getAttributes.getOrElse("signalValue", "0")

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Might factor these out too.

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fnothaft May 19, 2016

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Might factor these out too.

Show outdated Hide outdated ...st/scala/org/bdgenomics/adam/rdd/features/FeatureRDDFunctionsSuite.scala
import org.bdgenomics.formats.avro._
import org.scalactic.{ Equivalence, TypeCheckedTripleEquals }
object FeatureRDDFunctionsSuiteHelper {

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The functions in this object seem like they'd be useful to surface outside of the test scope.

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The functions in this object seem like they'd be useful to surface outside of the test scope.

Show outdated Hide outdated ...st/scala/org/bdgenomics/adam/rdd/features/FeatureRDDFunctionsSuite.scala
}
class FeatureRDDFunctionsSuiteHelper extends Serializable {
// empty

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What's this here for?

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What's this here for?

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heuermh May 19, 2016

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Adds the Serializable marker, otherwise tests will error

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Adds the Serializable marker, otherwise tests will error

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You can just add that to the singleton object, no? E.g., object FeatureRDDFunctionsSuiteHelper extends Serializable

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You can just add that to the singleton object, no? E.g., object FeatureRDDFunctionsSuiteHelper extends Serializable

Show outdated Hide outdated ...st/scala/org/bdgenomics/adam/rdd/features/FeatureRDDFunctionsSuite.scala
}
/*
sparkTest("round trip IntervalList format") {

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Eliminate dead test code, or change to an ignored test --> ignore("round trip..."){

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Eliminate dead test code, or change to an ignored test --> ignore("round trip..."){

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LGTM! I just made a pass through with a variety of nits.

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fnothaft commented May 19, 2016

LGTM! I just made a pass through with a variety of nits.

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Build result: FAILURE

GitHub pull request #998 of commit 8c212da 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 4f03eb4 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 4f03eb4 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 4f03eb49e355afd1765b413d1f1442ea02dac6e0First 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.

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GitHub pull request #998 of commit 8c212da 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 4f03eb4 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 4f03eb4 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 4f03eb49e355afd1765b413d1f1442ea02dac6e0First 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'
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@heuermh when do you think we can wrap this by?

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fnothaft commented Jun 3, 2016

@heuermh when do you think we can wrap this by?

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GitHub pull request #998 of commit dc491ae 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains f1ad9fb # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision f1ad9fb (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f f1ad9fbc852ed49d66a938228e210a2aeb1c8b00First 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'
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GitHub pull request #998 of commit dc491ae 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains f1ad9fb # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision f1ad9fb (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f f1ad9fbc852ed49d66a938228e210a2aeb1c8b00First 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'
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Updated with GFF3 support and addressed some comments above.

Still left to do:

  • Continue refactoring FeatureParserto reuse functionality where appropriate and improve consistency between formats
  • Refactor toGenes to use new proposed feature fields (geneId, transcriptId, and exonId) instead of attributes
  • -single file support, if that might be desirable
  • Writing header for IntervalList and GFF3 formats

Depends on bigdatagenomics/bdg-formats#82

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heuermh commented Jun 3, 2016

Updated with GFF3 support and addressed some comments above.

Still left to do:

  • Continue refactoring FeatureParserto reuse functionality where appropriate and improve consistency between formats
  • Refactor toGenes to use new proposed feature fields (geneId, transcriptId, and exonId) instead of attributes
  • -single file support, if that might be desirable
  • Writing header for IntervalList and GFF3 formats

Depends on bigdatagenomics/bdg-formats#82

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GitHub pull request #998 of commit 2f260e4 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 7783adc282593f152f6a034b7c5371f54a3bf45b # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 7783adc282593f152f6a034b7c5371f54a3bf45b (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 7783adc282593f152f6a034b7c5371f54a3bf45bFirst 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'
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GitHub pull request #998 of commit 2f260e4 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 7783adc282593f152f6a034b7c5371f54a3bf45b # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 7783adc282593f152f6a034b7c5371f54a3bf45b (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 7783adc282593f152f6a034b7c5371f54a3bf45bFirst 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'
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GitHub pull request #998 of commit fd68ccc 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 511ddd9484d32b5198010244f33a1fe975170df6 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 511ddd9484d32b5198010244f33a1fe975170df6 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 511ddd9484d32b5198010244f33a1fe975170df6First 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'
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GitHub pull request #998 of commit fd68ccc 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 511ddd9484d32b5198010244f33a1fe975170df6 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 511ddd9484d32b5198010244f33a1fe975170df6 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 511ddd9484d32b5198010244f33a1fe975170df6First 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'
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GitHub pull request #998 of commit fd1e8e2 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains d0eff44 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision d0eff44 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f d0eff44fdac1d0d2459d8100ae5b3e806517679cFirst 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'
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Build result: FAILURE

GitHub pull request #998 of commit fd1e8e2 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains d0eff44 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision d0eff44 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f d0eff44fdac1d0d2459d8100ae5b3e806517679cFirst 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.

@heuermh heuermh modified the milestone: 0.20.0 Jun 5, 2016

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GitHub pull request #998 of commit fa0f17f 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains d07a7e8 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision d07a7e8 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f d07a7e8f1e210681c3d25fb1eade7a21350822a6First 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.

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Build result: FAILURE

GitHub pull request #998 of commit fa0f17f 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains d07a7e8 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision d07a7e8 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f d07a7e8f1e210681c3d25fb1eade7a21350822a6First 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.

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Build result: FAILURE

GitHub pull request #998 of commit ae89357.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 ae89357^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains ae89357 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/head^{commit} # timeout=10Checking out Revision ae89357 (origin/pr/998/head) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f ae89357cd5344a349c57228b5b818fe9a0039832First 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.

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Build result: FAILURE

GitHub pull request #998 of commit ae89357.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 ae89357^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains ae89357 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/head^{commit} # timeout=10Checking out Revision ae89357 (origin/pr/998/head) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f ae89357cd5344a349c57228b5b818fe9a0039832First 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.

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Build result: FAILURE

GitHub pull request #998 of commit aa5b867 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains a0e77fb619019140b03bfdf6aa3e9f60dc1dee92 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision a0e77fb619019140b03bfdf6aa3e9f60dc1dee92 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f a0e77fb619019140b03bfdf6aa3e9f60dc1dee92First 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.

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Build result: FAILURE

GitHub pull request #998 of commit aa5b867 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains a0e77fb619019140b03bfdf6aa3e9f60dc1dee92 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision a0e77fb619019140b03bfdf6aa3e9f60dc1dee92 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f a0e77fb619019140b03bfdf6aa3e9f60dc1dee92First 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.

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Build result: FAILURE

GitHub pull request #998 of commit 65d3d22 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains f0d387b9f2719548c7d80103add98614b21dfbb8 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision f0d387b9f2719548c7d80103add98614b21dfbb8 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f f0d387b9f2719548c7d80103add98614b21dfbb8 > /home/jenkins/git2/bin/git rev-list a0e77fb619019140b03bfdf6aa3e9f60dc1dee92 # 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'
Test FAILed.

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Build result: FAILURE

GitHub pull request #998 of commit 65d3d22 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains f0d387b9f2719548c7d80103add98614b21dfbb8 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision f0d387b9f2719548c7d80103add98614b21dfbb8 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f f0d387b9f2719548c7d80103add98614b21dfbb8 > /home/jenkins/git2/bin/git rev-list a0e77fb619019140b03bfdf6aa3e9f60dc1dee92 # 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'
Test FAILed.

Show outdated Hide outdated ...rc/main/scala/org/bdgenomics/adam/rdd/features/FeatureRDDFunctions.scala
}
def saveAsIntervalList(fileName: String) = {
def escape(entry: (Any, Any)): String = {

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Where does escape get used? Perhaps I'm just missing things but I don't see it get called anywhere.

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fnothaft Jun 14, 2016

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Where does escape get used? Perhaps I'm just missing things but I don't see it get called anywhere.

Show outdated Hide outdated ...rc/main/scala/org/bdgenomics/adam/rdd/features/FeatureRDDFunctions.scala
f.getEnd,
f.getFeatureType,
// try exon_id first
Option(f.getExonId).getOrElse("~"),

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Is there any significance to ~? I would document.

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Is there any significance to ~? I would document.

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do nulls sort first or last in scala? I'm used to e.g. Ordering.nullsFirst in Guava.

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heuermh Jun 14, 2016

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do nulls sort first or last in scala? I'm used to e.g. Ordering.nullsFirst in Guava.

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Not sure. I was figuring that this was to handle the null case. If so, can you add a line comment to indicate so?

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Not sure. I was figuring that this was to handle the null case. If so, can you add a line comment to indicate so?

Show outdated Hide outdated ...rc/main/scala/org/bdgenomics/adam/rdd/features/FeatureRDDFunctions.scala
Option(f.getExonId).getOrElse("~"),
// then try transcript_id and exon_number
Option(f.getTranscriptId).getOrElse("~"),
f.getAttributes.getOrElse("exon_number", Int.MaxValue.toString).toInt

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Prefer f.getAttributes.get("exon_number").map(_.toInt).getOrElse(Int.MaxValue)

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Prefer f.getAttributes.get("exon_number").map(_.toInt).getOrElse(Int.MaxValue)

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nulls don't work in scala Ordering, and this line doesn't compile or handle nulls

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nulls don't work in scala Ordering, and this line doesn't compile or handle nulls

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Ah, sorry I mentally had the return type of f.getAttributes as a Scala Map. f.getAttributes returns a java.util.String, right? If you convert this return value into a Scala Map (e.g., via scala.collection.JavaConversions or etc), .get("exon_number") returns an Option[String], and then the .getOrElse handles the null case, no?

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Ah, sorry I mentally had the return type of f.getAttributes as a Scala Map. f.getAttributes returns a java.util.String, right? If you convert this return value into a Scala Map (e.g., via scala.collection.JavaConversions or etc), .get("exon_number") returns an Option[String], and then the .getOrElse handles the null case, no?

Show outdated Hide outdated adam-core/src/main/scala/org/bdgenomics/adam/rdd/features/Features.scala
package org.bdgenomics.adam.rdd.features
import scala.collection.JavaConversions._

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Nit: whitespace.

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Nit: whitespace.

Show outdated Hide outdated adam-core/src/main/scala/org/bdgenomics/adam/rdd/features/Features.scala
import scala.collection.mutable.HashMap
import scala.collection.mutable.MutableList
import org.bdgenomics.formats.avro.{ Dbxref, Feature, OntologyTerm, Strand }

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Nit: import sort order --> org before scala.

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Nit: import sort order --> org before scala.

Show outdated Hide outdated adam-core/src/main/scala/org/bdgenomics/adam/rdd/features/Features.scala
* @param strand strand to convert
* @return the specified strand converted to its string value
*/
def toString(strand: Strand): String = {

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I would avoid toString as a function name for Singleton objects.

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I would avoid toString as a function name for Singleton objects.

Show outdated Hide outdated adam-core/src/main/scala/org/bdgenomics/adam/rdd/features/Features.scala
import scala.collection.JavaConversions._
import scala.collection.mutable.ArrayBuffer

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Prefer import scala.collection.mutable.{...} to imports from same package across multiple lines.

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fnothaft Jun 14, 2016

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Prefer import scala.collection.mutable.{...} to imports from same package across multiple lines.

Show outdated Hide outdated adam-core/src/main/scala/org/bdgenomics/adam/rdd/features/Features.scala
* @param dbxref database cross reference to convert
* @return the specified database cross reference converted to its string value
*/
def toString(dbxref: Dbxref): String = {

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Ditto RE naming of toString.

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fnothaft Jun 14, 2016

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Ditto RE naming of toString.

Show outdated Hide outdated adam-core/src/main/scala/org/bdgenomics/adam/rdd/features/Features.scala
* @param ontologyTerm ontology term to convert
* @return the specified ontology term converted to its string value
*/
def toString(ontologyTerm: OntologyTerm): String = {

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Ditto

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Show outdated Hide outdated adam-core/src/main/scala/org/bdgenomics/adam/rdd/features/Features.scala
}
// set remaining attributes if non-empty;
// any duplicate keys are lost at this point, last one in wins

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Would it make sense to log duplicate keys?

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Would it make sense to log duplicate keys?

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heuermh Jun 14, 2016

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+1, will add logging

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heuermh Jun 14, 2016

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+1, will add logging

Show outdated Hide outdated adam-core/src/main/scala/org/bdgenomics/adam/rdd/features/Features.scala
attrs += Tuple2("Is_circular", b.toString)
}
// ... and why Tuple2 is required here

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fnothaft Jun 14, 2016

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OOC, does it compile OK if you don't use an anon argument? E.g., does Option(feature.getFeatureId).foreach(id => attrs += ("ID", id)) compile?

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OOC, does it compile OK if you don't use an anon argument? E.g., does Option(feature.getFeatureId).foreach(id => attrs += ("ID", id)) compile?

Option(feature.getGeneId).foreach(attrs += Tuple2("gene_id", _))
Option(feature.getTranscriptId).foreach(attrs += Tuple2("transcript_id", _))
Option(feature.getExonId).foreach(attrs += Tuple2("exon_id", _))
for (alias <- feature.getAliases) attrs += Tuple2("Alias", alias)

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I generally prefer feature.getAliases.foreach to for (...), but that's just me.

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I generally prefer feature.getAliases.foreach to for (...), but that's just me.

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I don't think that worked before, maybe for the same anon argument issue you mention above. Will give it a try.

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I don't think that worked before, maybe for the same anon argument issue you mention above. Will give it a try.

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You'd need to convert the java.util.List into a Scala collection for it to work.

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You'd need to convert the java.util.List into a Scala collection for it to work.

* @return a name for the specified feature considering its attributes
*/
def nameOf(feature: Feature): String = {
Option(feature.getName).foreach(return _)

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I strongly dislike explicit returns in Scala code. I would rather:

def nameOf(feature: Feature): String = {
  Option(feature.getName).getOrElse(
    Option(feature.getFeatureId).getOrElse(feature.getFeatureType match {
      case "exon" => Option(feature.getExonId)
      case "transcript" => Option(feature.getTranscriptId)
      case "gene" => Option(feature.getGeneId)
      case s: String => Some(s)
      case _ => None
    }.getOrElse("feature")))
}
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I strongly dislike explicit returns in Scala code. I would rather:

def nameOf(feature: Feature): String = {
  Option(feature.getName).getOrElse(
    Option(feature.getFeatureId).getOrElse(feature.getFeatureType match {
      case "exon" => Option(feature.getExonId)
      case "transcript" => Option(feature.getTranscriptId)
      case "gene" => Option(feature.getGeneId)
      case s: String => Some(s)
      case _ => None
    }.getOrElse("feature")))
}

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heuermh Jun 14, 2016

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this and various permutations doesn't work for me; compile errors or value getOrElse is not a member of java.io.Serializable

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this and various permutations doesn't work for me; compile errors or value getOrElse is not a member of java.io.Serializable

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Just made a pass. Overall, LGTM! Dropped various style nits and the like inline.

I'd be ok pushing this and adding -single and header support later.

I +1.

Also, this adds all the code needed for handling the changes in bigdatagenomics/bdg-formats#82, correct?

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fnothaft commented Jun 14, 2016

Just made a pass. Overall, LGTM! Dropped various style nits and the like inline.

I'd be ok pushing this and adding -single and header support later.

I +1.

Also, this adds all the code needed for handling the changes in bigdatagenomics/bdg-formats#82, correct?

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Test FAILed.
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Build result: FAILURE

GitHub pull request #998 of commit 0948bf2 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 3bdd3ca832b784d31332b73b82a804f2acb2c718 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 3bdd3ca832b784d31332b73b82a804f2acb2c718 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 3bdd3ca832b784d31332b73b82a804f2acb2c718 > /home/jenkins/git2/bin/git rev-list 2579282e083482e1d781ec622231a24f601e1aa1 # 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'
Test FAILed.

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Build result: FAILURE

GitHub pull request #998 of commit 0948bf2 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 3bdd3ca832b784d31332b73b82a804f2acb2c718 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 3bdd3ca832b784d31332b73b82a804f2acb2c718 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 3bdd3ca832b784d31332b73b82a804f2acb2c718 > /home/jenkins/git2/bin/git rev-list 2579282e083482e1d781ec622231a24f601e1aa1 # 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'
Test FAILed.

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Addressed most review comments and rebased.

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heuermh commented Jun 15, 2016

Addressed most review comments and rebased.

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Build result: FAILURE

GitHub pull request #998 of commit fd43334 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 446f4707d04574442db241eab65bb484835fcbd0 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 446f4707d04574442db241eab65bb484835fcbd0 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 446f4707d04574442db241eab65bb484835fcbd0 > /home/jenkins/git2/bin/git rev-list 3bdd3ca832b784d31332b73b82a804f2acb2c718 # 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'
Test FAILed.

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Build result: FAILURE

GitHub pull request #998 of commit fd43334 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 446f4707d04574442db241eab65bb484835fcbd0 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 446f4707d04574442db241eab65bb484835fcbd0 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 446f4707d04574442db241eab65bb484835fcbd0 > /home/jenkins/git2/bin/git rev-list 3bdd3ca832b784d31332b73b82a804f2acb2c718 # 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'
Test FAILed.

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Jenkins, test this please.

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fnothaft commented Jun 15, 2016

Jenkins, test this please.

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Build result: FAILURE

GitHub pull request #998 of commit fd43334 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 446f4707d04574442db241eab65bb484835fcbd0 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 446f4707d04574442db241eab65bb484835fcbd0 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 446f4707d04574442db241eab65bb484835fcbd0 > /home/jenkins/git2/bin/git rev-list 446f4707d04574442db241eab65bb484835fcbd0 # 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'
Test FAILed.

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Test FAILed.
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Build result: FAILURE

GitHub pull request #998 of commit fd43334 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 446f4707d04574442db241eab65bb484835fcbd0 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 446f4707d04574442db241eab65bb484835fcbd0 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 446f4707d04574442db241eab65bb484835fcbd0 > /home/jenkins/git2/bin/git rev-list 446f4707d04574442db241eab65bb484835fcbd0 # 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'
Test FAILed.

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The unit test failure is due to indeterminate sorting. Is there a way to easily sort by deep compare (nested arrays and maps)?

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heuermh commented Jun 15, 2016

The unit test failure is due to indeterminate sorting. Is there a way to easily sort by deep compare (nested arrays and maps)?

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Build result: FAILURE

GitHub pull request #998 of commit a2a688c 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 0660916dbadb4f13232ff50ed053042689f8b380 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 0660916dbadb4f13232ff50ed053042689f8b380 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 0660916dbadb4f13232ff50ed053042689f8b380 > /home/jenkins/git2/bin/git rev-list 446f4707d04574442db241eab65bb484835fcbd0 # 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'
Test FAILed.

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Test FAILed.
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Build result: FAILURE

GitHub pull request #998 of commit a2a688c 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 0660916dbadb4f13232ff50ed053042689f8b380 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 0660916dbadb4f13232ff50ed053042689f8b380 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 0660916dbadb4f13232ff50ed053042689f8b380 > /home/jenkins/git2/bin/git rev-list 446f4707d04574442db241eab65bb484835fcbd0 # 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'
Test FAILed.

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Maybe that's not the problem. I don't see this test failure locally.

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heuermh commented Jun 15, 2016

Maybe that's not the problem. I don't see this test failure locally.

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Test FAILed.
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Build result: FAILURE

GitHub pull request #998 of commit 1c1fe23 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 95ea3c23796024c70a81ce78474b6601a9690ce6 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 95ea3c23796024c70a81ce78474b6601a9690ce6 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 95ea3c23796024c70a81ce78474b6601a9690ce6 > /home/jenkins/git2/bin/git rev-list 0660916dbadb4f13232ff50ed053042689f8b380 # 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'
Test FAILed.

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Test FAILed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1277/

Build result: FAILURE

GitHub pull request #998 of commit 1c1fe23 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 95ea3c23796024c70a81ce78474b6601a9690ce6 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 95ea3c23796024c70a81ce78474b6601a9690ce6 (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 95ea3c23796024c70a81ce78474b6601a9690ce6 > /home/jenkins/git2/bin/git rev-list 0660916dbadb4f13232ff50ed053042689f8b380 # 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'
Test FAILed.

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Test FAILed.
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Build result: FAILURE

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

AmplabJenkins commented Jun 16, 2016

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

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

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Jenkins, test this please.

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heuermh commented Jun 17, 2016

Jenkins, test this please.

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Test PASSed.
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Test PASSed.

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Test PASSed.
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Test PASSed.

@heuermh heuermh added ready to merge and removed needs work labels Jun 22, 2016

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bdg-formats 0.9.0 has pushed. Can you update the dependency, rebase, and push? I'll merge on passing tests.

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fnothaft commented Jun 27, 2016

bdg-formats 0.9.0 has pushed. Can you update the dependency, rebase, and push? I'll merge on passing tests.

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Test FAILed.
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Build result: FAILURE

GitHub pull request #998 of commit d78910d 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 8ca998a # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 8ca998a (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 8ca998a > /home/jenkins/git2/bin/git rev-list 317561754912b3f81306fd1c564265f027e5e574 # 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'
Test FAILed.

AmplabJenkins commented Jun 27, 2016

Test FAILed.
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Build result: FAILURE

GitHub pull request #998 of commit d78910d 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/998/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 8ca998a # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/998/merge^{commit} # timeout=10Checking out Revision 8ca998a (origin/pr/998/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 8ca998a > /home/jenkins/git2/bin/git rev-list 317561754912b3f81306fd1c564265f027e5e574 # 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'
Test FAILed.

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Jenkins, retest this please.

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fnothaft commented Jun 27, 2016

Jenkins, retest this please.

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Test PASSed.
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Test PASSed.

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Test PASSed.
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Test PASSed.

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Thanks @heuermh! I've squashed this down to a single commit and merged as 8abb47a.

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fnothaft commented Jun 28, 2016

Thanks @heuermh! I've squashed this down to a single commit and merged as 8abb47a.

@fnothaft fnothaft closed this Jun 28, 2016

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Thanks!

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heuermh commented Jun 28, 2016

Thanks!

@heuermh heuermh deleted the heuermh:feature-writers branch Jun 28, 2016

@heuermh heuermh referenced this pull request Jun 28, 2016

Closed

Support GFF3 format #1007

@heuermh heuermh removed the ready to merge label Jun 28, 2016

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