Clean rewrite of VariantContextConverter #1288

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fnothaft commented Nov 23, 2016

Resolves #1107:

  • Clean rewrite of VariantContextConverter. Now, there's a conversion function per field, pretty much, and the conversion process is pretty much pure functional, which is kinda cool!
  • Adds support for arbitrary attributes as defined in the header lines.
  • Supports all of the fields in the schema except for those slated to be dropped in bigdatagenomics/bdg-formats#108.
  • Added 58 tests! w00t!

Also see samtools/htsjdk#751.

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I need to make a pass and clean up the docs on this, otherwise it is all good to go.

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fnothaft commented Nov 23, 2016

I need to make a pass and clean up the docs on this, otherwise it is all good to go.

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@@ -63,10 +108,72 @@ private[adam] object SupportedHeaderLines {
transcriptEffects
)
+ lazy val genotype = VCFStandardHeaderLines.getFormatLine(
+ VCFConstants.GENOTYPE_KEY)

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heuermh Nov 23, 2016

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These keys and "StandardHeaderLines" can't be trusted. We should define our own here rather than depending on htsjdk.

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These keys and "StandardHeaderLines" can't be trusted. We should define our own here rather than depending on htsjdk.

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I think I'm OK trusting the GT format line, but if you feel strongly enough about it, I'll rewrite that one too. ;)

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fnothaft Nov 23, 2016

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I think I'm OK trusting the GT format line, but if you feel strongly enough about it, I'll rewrite that one too. ;)

+ // note: this is not spec compliant!
+ // however, this is due to a bug in htsjdk --> https://github.com/samtools/htsjdk/issues/751
+ // the standard header lines get populated no matter what the header lines are on the
+ // file. not clear how to disable this...

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This is why we need to overwrite the standard headers when writing as VCF. Are you saying it also causes trouble when reading in?

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This is why we need to overwrite the standard headers when writing as VCF. Are you saying it also causes trouble when reading in?

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Yeah, I wasted an hour on this last night. The relevant code path is https://github.com/samtools/htsjdk/blob/master/src/main/java/htsjdk/variant/vcf/AbstractVCFCodec.java#L224. If your header line disagrees with the standard header line, HTSJDK clobbers it by default. We can disable that, but I don't think Hadoop-BAM supports disabling the header line clobbering.

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Yeah, I wasted an hour on this last night. The relevant code path is https://github.com/samtools/htsjdk/blob/master/src/main/java/htsjdk/variant/vcf/AbstractVCFCodec.java#L224. If your header line disagrees with the standard header line, HTSJDK clobbers it by default. We can disable that, but I don't think Hadoop-BAM supports disabling the header line clobbering.

@@ -1,323 +0,0 @@
-/**

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heuermh Nov 23, 2016

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woot!

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woot!

+ }
+ }
+
+ private def tryAndCatchStringCast[T](attr: java.lang.Object,

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sigh

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This was another hour of pain last night.

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This was another hour of pain last night.

+ // see https://github.com/samtools/htsjdk/issues/741
+ val gtFiltersWereApplied = true
+ if (gtFiltersWereApplied) {
+ val filtersWereApplied = vcab.setFiltersApplied(true)

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renaming the builder reads a bit screwy to me

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renaming the builder reads a bit screwy to me

@@ -934,9 +934,10 @@ class ADAMContext private (@transient val sc: SparkContext) extends Serializable
// load vcf metadata
val (sd, samples, headers) = loadVcfMetadata(filePath)
- val vcc = new VariantContextConverter(Some(sd))
+ val vcc = new VariantContextConverter()
+ val convFn = vcc.makeHtsjdkGenotypeConverter(headers)

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heuermh Nov 23, 2016

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I assume we're going to have HtsjdkVariantContextVariant and HtsjdkVariantContextVariantAnnotation conversion functions shortly, what is the point of VariantContextConverter then?

Why not pass headers (after modifications), htsjdk context, and stringency into separate Converter classes/objects? convFn seems like it should be hidden from the API to me, unless there are caller-modifiable parts to it.

In bdg-convert I have something like

val vc = VariantConverter
val vac = VariantAnnotationConverter(vc)
val gc = GenotypeConverter(vc, vac) // or GenotypeConverter(vc)
val gac = GenotypeAnnotationConverter(vc, vac, gc) // or GenotypeConverter(vc, gc)

all which are stateless and immutable and implement T convert(S, Logger, Stringency) throws ConversionException.

In this case S could be (VcfHeader, HtsjdkVariantContext) and Iterable[Variant], Iterable[VariantAnnotation], Iterable[Genotype], or Iterable[GenotypeAnnotation] respectively for T, with back references filled in accordingly. It might also be useful to support projections.

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heuermh Nov 23, 2016

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I assume we're going to have HtsjdkVariantContextVariant and HtsjdkVariantContextVariantAnnotation conversion functions shortly, what is the point of VariantContextConverter then?

Why not pass headers (after modifications), htsjdk context, and stringency into separate Converter classes/objects? convFn seems like it should be hidden from the API to me, unless there are caller-modifiable parts to it.

In bdg-convert I have something like

val vc = VariantConverter
val vac = VariantAnnotationConverter(vc)
val gc = GenotypeConverter(vc, vac) // or GenotypeConverter(vc)
val gac = GenotypeAnnotationConverter(vc, vac, gc) // or GenotypeConverter(vc, gc)

all which are stateless and immutable and implement T convert(S, Logger, Stringency) throws ConversionException.

In this case S could be (VcfHeader, HtsjdkVariantContext) and Iterable[Variant], Iterable[VariantAnnotation], Iterable[Genotype], or Iterable[GenotypeAnnotation] respectively for T, with back references filled in accordingly. It might also be useful to support projections.

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I generally agree that the interface is a crufty. My goal here was to clean up the guts of VariantContextConverter first. That being said, we might as well do it in one pass.

convFn seems like it should be hidden from the API to me, unless there are caller-modifiable parts to it.

I agree.

Why not pass headers (after modifications), htsjdk context, and stringency into separate Converter classes/objects?

WRT headers, a small (but significant) optimization is to only build the conversion function once. Thus the headers should be passed to the class constructor.

Otherwise, I agree.

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fnothaft Nov 23, 2016

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I generally agree that the interface is a crufty. My goal here was to clean up the guts of VariantContextConverter first. That being said, we might as well do it in one pass.

convFn seems like it should be hidden from the API to me, unless there are caller-modifiable parts to it.

I agree.

Why not pass headers (after modifications), htsjdk context, and stringency into separate Converter classes/objects?

WRT headers, a small (but significant) optimization is to only build the conversion function once. Thus the headers should be passed to the class constructor.

Otherwise, I agree.

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Let me try to fix up these interfaces, I'll ping back here later.

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fnothaft Nov 23, 2016

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Let me try to fix up these interfaces, I'll ping back here later.

+
+ private[converters] def extractFilters(vca: VariantCallingAnnotations,
+ gb: GenotypeBuilder): GenotypeBuilder = {
+ Option(vca.getFiltersApplied)

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This is probably correct, but is much harder to read than the non-functional way it is written for Variant filters. Sorry, I'm getting old. :)

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This is probably correct, but is much harder to read than the non-functional way it is written for Variant filters. Sorry, I'm getting old. :)

+ Array(0, 1, 2)).build
+ }
+
+ test("no phasing set going htsjdk->adam") {

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heuermh Nov 23, 2016

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these tests are nice

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these tests are nice

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Thank you!

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Thank you!

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Initial review pass.

I like the conversion functions and the way they are executed inside VariantContextConverter but am less convinced of the API at a higher level, especially considering changes I'll need to make shortly for Variant and VariantAnnotation.

We'll also want some way to limit code duplication for similar conversions (i.e. between INFO fields on VariantAnnotation and FORMAT fields on Genotype and GenotypeAnnotation).

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heuermh commented Nov 23, 2016

Initial review pass.

I like the conversion functions and the way they are executed inside VariantContextConverter but am less convinced of the API at a higher level, especially considering changes I'll need to make shortly for Variant and VariantAnnotation.

We'll also want some way to limit code duplication for similar conversions (i.e. between INFO fields on VariantAnnotation and FORMAT fields on Genotype and GenotypeAnnotation).

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We'll also want some way to limit code duplication for similar conversions (i.e. between INFO fields on VariantAnnotation and FORMAT fields on Genotype and GenotypeAnnotation).

It would be nice if the htsjdk Genotype and VariantContext attribute access APIs weren't nonsensically different, wouldn't it?

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fnothaft commented Nov 23, 2016

We'll also want some way to limit code duplication for similar conversions (i.e. between INFO fields on VariantAnnotation and FORMAT fields on Genotype and GenotypeAnnotation).

It would be nice if the htsjdk Genotype and VariantContext attribute access APIs weren't nonsensically different, wouldn't it?

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@heuermh I've resolved your comments.

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fnothaft commented Dec 9, 2016

@heuermh I've resolved your comments.

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[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /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 c9567a1^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains c9567a1 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1288/head^{commit} # timeout=10Checking out Revision c9567a1 (origin/pr/1288/head) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f c9567a1027559d79b9d4acc8c6464a693d59f913First 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 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /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 c9567a1^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains c9567a1 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1288/head^{commit} # timeout=10Checking out Revision c9567a1 (origin/pr/1288/head) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f c9567a1027559d79b9d4acc8c6464a693d59f913First 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'
Test FAILed.

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[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /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/1288/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains f29a9da5ca0967ee35e3e3791cbdbe9037c5a1e1 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1288/merge^{commit} # timeout=10Checking out Revision f29a9da5ca0967ee35e3e3791cbdbe9037c5a1e1 (origin/pr/1288/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f f29a9da5ca0967ee35e3e3791cbdbe9037c5a1e1First 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 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /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/1288/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains f29a9da5ca0967ee35e3e3791cbdbe9037c5a1e1 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1288/merge^{commit} # timeout=10Checking out Revision f29a9da5ca0967ee35e3e3791cbdbe9037c5a1e1 (origin/pr/1288/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f f29a9da5ca0967ee35e3e3791cbdbe9037c5a1e1First 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'
Test FAILed.

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[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /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/1288/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 62b04a8913ce49281e054550e3994c65c6495e17 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1288/merge^{commit} # timeout=10Checking out Revision 62b04a8913ce49281e054550e3994c65c6495e17 (origin/pr/1288/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 62b04a8913ce49281e054550e3994c65c6495e17 > /home/jenkins/git2/bin/git rev-list f29a9da5ca0967ee35e3e3791cbdbe9037c5a1e1 # timeout=10Triggering 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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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1671/

Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /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/1288/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 62b04a8913ce49281e054550e3994c65c6495e17 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1288/merge^{commit} # timeout=10Checking out Revision 62b04a8913ce49281e054550e3994c65c6495e17 (origin/pr/1288/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 62b04a8913ce49281e054550e3994c65c6495e17 > /home/jenkins/git2/bin/git rev-list f29a9da5ca0967ee35e3e3791cbdbe9037c5a1e1 # timeout=10Triggering 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'
Test FAILed.

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Jenkins, retest this please.

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fnothaft commented Dec 9, 2016

Jenkins, retest this please.

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1672/

Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /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/1288/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 62b04a8913ce49281e054550e3994c65c6495e17 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1288/merge^{commit} # timeout=10Checking out Revision 62b04a8913ce49281e054550e3994c65c6495e17 (origin/pr/1288/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 62b04a8913ce49281e054550e3994c65c6495e17 > /home/jenkins/git2/bin/git rev-list 62b04a8913ce49281e054550e3994c65c6495e17 # timeout=10Triggering 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'
Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1672/

Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /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/1288/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 62b04a8913ce49281e054550e3994c65c6495e17 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1288/merge^{commit} # timeout=10Checking out Revision 62b04a8913ce49281e054550e3994c65c6495e17 (origin/pr/1288/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 62b04a8913ce49281e054550e3994c65c6495e17 > /home/jenkins/git2/bin/git rev-list 62b04a8913ce49281e054550e3994c65c6495e17 # timeout=10Triggering 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'
Test FAILed.

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1673/

Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /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/1288/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 6c04100ed742470e1f21c75c51a7b96ef6498ba3 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1288/merge^{commit} # timeout=10Checking out Revision 6c04100ed742470e1f21c75c51a7b96ef6498ba3 (origin/pr/1288/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 6c04100ed742470e1f21c75c51a7b96ef6498ba3 > /home/jenkins/git2/bin/git rev-list 62b04a8913ce49281e054550e3994c65c6495e17 # timeout=10Triggering 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'
Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1673/

Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /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/1288/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 6c04100ed742470e1f21c75c51a7b96ef6498ba3 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1288/merge^{commit} # timeout=10Checking out Revision 6c04100ed742470e1f21c75c51a7b96ef6498ba3 (origin/pr/1288/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 6c04100ed742470e1f21c75c51a7b96ef6498ba3 > /home/jenkins/git2/bin/git rev-list 62b04a8913ce49281e054550e3994c65c6495e17 # timeout=10Triggering 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'
Test FAILed.

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Jenkins, retest this please.

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fnothaft commented Dec 9, 2016

Jenkins, retest this please.

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1674/

Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /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/1288/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 6c04100ed742470e1f21c75c51a7b96ef6498ba3 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1288/merge^{commit} # timeout=10Checking out Revision 6c04100ed742470e1f21c75c51a7b96ef6498ba3 (origin/pr/1288/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 6c04100ed742470e1f21c75c51a7b96ef6498ba3 > /home/jenkins/git2/bin/git rev-list 6c04100ed742470e1f21c75c51a7b96ef6498ba3 # timeout=10Triggering 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'
Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1674/

Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /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/1288/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 6c04100ed742470e1f21c75c51a7b96ef6498ba3 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1288/merge^{commit} # timeout=10Checking out Revision 6c04100ed742470e1f21c75c51a7b96ef6498ba3 (origin/pr/1288/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 6c04100ed742470e1f21c75c51a7b96ef6498ba3 > /home/jenkins/git2/bin/git rev-list 6c04100ed742470e1f21c75c51a7b96ef6498ba3 # timeout=10Triggering 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'
Test FAILed.

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1675/

Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /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/1288/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains fd4ebfb # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1288/merge^{commit} # timeout=10Checking out Revision fd4ebfb (origin/pr/1288/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f fd4ebfb > /home/jenkins/git2/bin/git rev-list 6c04100ed742470e1f21c75c51a7b96ef6498ba3 # timeout=10Triggering 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'
Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1675/

Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /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/1288/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains fd4ebfb # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1288/merge^{commit} # timeout=10Checking out Revision fd4ebfb (origin/pr/1288/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f fd4ebfb > /home/jenkins/git2/bin/git rev-list 6c04100ed742470e1f21c75c51a7b96ef6498ba3 # timeout=10Triggering 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'
Test FAILed.

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The failing unit test needs to be changed to no longer search for "flatten" in the --help text.

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heuermh commented Dec 9, 2016

The failing unit test needs to be changed to no longer search for "flatten" in the --help text.

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Yeah, I'd done that and then force pushed. Jenkins is doing that frustrating thing where it doesn't pick up force pushes correctly...

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fnothaft commented Dec 9, 2016

Yeah, I'd done that and then force pushed. Jenkins is doing that frustrating thing where it doesn't pick up force pushes correctly...

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Jenkins, retest this please.

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fnothaft commented Dec 9, 2016

Jenkins, retest this please.

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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1676/
Test PASSed.

Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1676/
Test PASSed.

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Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1680/
Test PASSed.

Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1680/
Test PASSed.

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This works end-to-end now, passes all tests, etc. I'm going to make a pass to do some method documentation cleanup, but let's get started reviewing this behemoth.

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fnothaft commented Dec 22, 2016

This works end-to-end now, passes all tests, etc. I'm going to make a pass to do some method documentation cleanup, but let's get started reviewing this behemoth.

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Otherwise, I'm going to start cutting a bdg-formats 0.10.1 release.

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fnothaft commented Dec 22, 2016

Otherwise, I'm going to start cutting a bdg-formats 0.10.1 release.

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[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /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/1288/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains cae4c0422e4d71a5937f260c7d5329148fbc34af # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1288/merge^{commit} # timeout=10Checking out Revision cae4c0422e4d71a5937f260c7d5329148fbc34af (origin/pr/1288/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f cae4c0422e4d71a5937f260c7d5329148fbc34af > /home/jenkins/git2/bin/git rev-list c6a2da7 # timeout=10Triggering 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 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /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/1288/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains cae4c0422e4d71a5937f260c7d5329148fbc34af # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1288/merge^{commit} # timeout=10Checking out Revision cae4c0422e4d71a5937f260c7d5329148fbc34af (origin/pr/1288/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f cae4c0422e4d71a5937f260c7d5329148fbc34af > /home/jenkins/git2/bin/git rev-list c6a2da7 # timeout=10Triggering 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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Jenkins, test this please.

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fnothaft commented Dec 22, 2016

Jenkins, test this please.

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Otherwise, I'm going to start cutting a bdg-formats 0.10.1 release.

Thanks for cutting this! Did you close the staging repo? I don't see it up on Maven Central yet.

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heuermh commented Dec 22, 2016

Otherwise, I'm going to start cutting a bdg-formats 0.10.1 release.

Thanks for cutting this! Did you close the staging repo? I don't see it up on Maven Central yet.

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Otherwise, I'm going to start cutting a bdg-formats 0.10.1 release.

Thanks for cutting this! Did you close the staging repo? I don't see it up on Maven Central yet.

Yeah, closed, released, dropped. It shows up OK in Sonatype, not sure why it hasn't pushed to Central yet. I typically see a 4-12 hour lag in the push, so I'm guessing it's just higher volume than usual with the end of year rush.

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fnothaft commented Dec 22, 2016

Otherwise, I'm going to start cutting a bdg-formats 0.10.1 release.

Thanks for cutting this! Did you close the staging repo? I don't see it up on Maven Central yet.

Yeah, closed, released, dropped. It shows up OK in Sonatype, not sure why it hasn't pushed to Central yet. I typically see a 4-12 hour lag in the push, so I'm guessing it's just higher volume than usual with the end of year rush.

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Heroic effort, my friend!

A few more things that may need to happen, we should triage to add on to this pull request, in a separate pull request for 0.21.0, or save until later release:

  • formatReadDepth and similar shouldn't set only reference value if the array is the wrong length
  • Exceptions thrown when parsing headers don't consider validation stringency (should they?)
  • convert(HtsjdkVariantContext): Seq[ADAMVariantContext] needs try/catch with validation stringency
  • Add unit tests for different ValidationStringencys
  • Remove val annotations: Option[VariantAnnotation] from VariantContext
  • Consider splitting VariantContextConverter into two classes, one for each direction
  • Merge Vcf2ADAM and ADAM2Vcf, then split into transformVariants and transformGenotypes
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heuermh commented Dec 22, 2016

Heroic effort, my friend!

A few more things that may need to happen, we should triage to add on to this pull request, in a separate pull request for 0.21.0, or save until later release:

  • formatReadDepth and similar shouldn't set only reference value if the array is the wrong length
  • Exceptions thrown when parsing headers don't consider validation stringency (should they?)
  • convert(HtsjdkVariantContext): Seq[ADAMVariantContext] needs try/catch with validation stringency
  • Add unit tests for different ValidationStringencys
  • Remove val annotations: Option[VariantAnnotation] from VariantContext
  • Consider splitting VariantContextConverter into two classes, one for each direction
  • Merge Vcf2ADAM and ADAM2Vcf, then split into transformVariants and transformGenotypes
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Here's my thoughts:

formatReadDepth and similar shouldn't set only reference value if the array is the wrong length
Exceptions thrown when parsing headers don't consider validation stringency (should they?)
convert(HtsjdkVariantContext): Seq[ADAMVariantContext] needs try/catch with validation stringency
Add unit tests for different ValidationStringencys
Remove val annotations: Option[VariantAnnotation] from VariantContext

These are fairly small; let's do these here.

Merge Vcf2ADAM and ADAM2Vcf, then split into transformVariants and transformGenotypes
Consider splitting VariantContextConverter into two classes, one for each direction

Let's triage these to a later release.

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fnothaft commented Dec 22, 2016

Here's my thoughts:

formatReadDepth and similar shouldn't set only reference value if the array is the wrong length
Exceptions thrown when parsing headers don't consider validation stringency (should they?)
convert(HtsjdkVariantContext): Seq[ADAMVariantContext] needs try/catch with validation stringency
Add unit tests for different ValidationStringencys
Remove val annotations: Option[VariantAnnotation] from VariantContext

These are fairly small; let's do these here.

Merge Vcf2ADAM and ADAM2Vcf, then split into transformVariants and transformGenotypes
Consider splitting VariantContextConverter into two classes, one for each direction

Let's triage these to a later release.

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As an aside, I've got this done:

Exceptions thrown when parsing headers don't consider validation stringency (should they?)

But it can't be tested, because there's only two cases where the headers throw exceptions:

  • Flag in FORMAT line
  • Multi-valued Flag in INFO line

and HTSJDK doesn't allow you to create the former, and if you try to create the latter, HTSJDK rewrites the header line to a single valued line, and of course, these behaviors are not overridable. I'm going to drop an ignored test inline documenting this.

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fnothaft commented Dec 23, 2016

As an aside, I've got this done:

Exceptions thrown when parsing headers don't consider validation stringency (should they?)

But it can't be tested, because there's only two cases where the headers throw exceptions:

  • Flag in FORMAT line
  • Multi-valued Flag in INFO line

and HTSJDK doesn't allow you to create the former, and if you try to create the latter, HTSJDK rewrites the header line to a single valued line, and of course, these behaviors are not overridable. I'm going to drop an ignored test inline documenting this.

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OK, this is good to go, short of the 0.10.1 release of bdg-formats pushing. I'm not sure why it still hasn't pushed to Maven Central. If I still don't see it in Maven Central by tomorrow morning, I'll open a JIRA with the Sonatype folks and we'll hopefully resolve it. The validation stringency tests are a bit weak; the only field that is easy to test is the SB field, so I've restricted my test to that for now.

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fnothaft commented Dec 23, 2016

OK, this is good to go, short of the 0.10.1 release of bdg-formats pushing. I'm not sure why it still hasn't pushed to Maven Central. If I still don't see it in Maven Central by tomorrow morning, I'll open a JIRA with the Sonatype folks and we'll hopefully resolve it. The validation stringency tests are a bit weak; the only field that is easy to test is the SB field, so I've restricted my test to that for now.

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[...truncated 38 lines...]Triggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
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[...truncated 38 lines...]Triggering ADAM-prb ? 2.6.0,2.11,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.5.2,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.3.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.4.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
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Merge Vcf2ADAM and ADAM2Vcf, then split into transformVariants and transformGenotypes

Let's triage these to a later release.

I'll take this one on later.

I'm going to drop an ignored test inline documenting [how much htsjdk sucks].

and

If I still don't see [bdg-formats] in Maven Central by tomorrow morning, I'll open a JIRA with the Sonatype folks and we'll hopefully resolve it.

Sounds good.

I see only one comment from above still unresolved (#1288 (comment)); I'll do a full review pass this evening.

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heuermh commented Dec 23, 2016

Merge Vcf2ADAM and ADAM2Vcf, then split into transformVariants and transformGenotypes

Let's triage these to a later release.

I'll take this one on later.

I'm going to drop an ignored test inline documenting [how much htsjdk sucks].

and

If I still don't see [bdg-formats] in Maven Central by tomorrow morning, I'll open a JIRA with the Sonatype folks and we'll hopefully resolve it.

Sounds good.

I see only one comment from above still unresolved (#1288 (comment)); I'll do a full review pass this evening.

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@fnothaft @jpdna @akmorrow13 @devin-petersohn Please review for code style, correctness, unit test coverage, and API documentation.

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heuermh commented Dec 23, 2016

@fnothaft @jpdna @akmorrow13 @devin-petersohn Please review for code style, correctness, unit test coverage, and API documentation.

@@ -1,82 +0,0 @@
-/**

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Just curious why this is being removed.

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Just curious why this is being removed.

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We don't use it anymore, we had a ticket (#1244) that was leaning towards removing it, and it started causing unit test failures (due to an issue I was hinting at in said ticket), so I went ahead and just got rid of it here.

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We don't use it anymore, we had a ticket (#1244) that was leaning towards removing it, and it started causing unit test failures (due to an issue I was hinting at in said ticket), so I went ahead and just got rid of it here.

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sounds good!

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sounds good!

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So interestingly enough, it looks like bdg-formats 0.10.1 pushed to Maven Central (http://search.maven.org/#artifactdetails%7Corg.bdgenomics.bdg-formats%7Cbdg-formats%7C0.10.1%7Cjar works), but doesn't show up if you search for the artifact. I'm guessing this is some weirdness with caching search results. Let me bump the bdg-formats dependency now.

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fnothaft commented Dec 23, 2016

So interestingly enough, it looks like bdg-formats 0.10.1 pushed to Maven Central (http://search.maven.org/#artifactdetails%7Corg.bdgenomics.bdg-formats%7Cbdg-formats%7C0.10.1%7Cjar works), but doesn't show up if you search for the artifact. I'm guessing this is some weirdness with caching search results. Let me bump the bdg-formats dependency now.

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@fnothaft Let me know if you want to chat on how we might want to squash commits and do the merge.

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heuermh commented Jan 4, 2017

@fnothaft Let me know if you want to chat on how we might want to squash commits and do the merge.

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@fnothaft Let me know if you want to chat on how we might want to squash commits and do the merge.

Sorry I couldn't make the call today. Let me make a pass over the commits and take a gander. Is this PR good to go from your side otherwise?

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fnothaft commented Jan 4, 2017

@fnothaft Let me know if you want to chat on how we might want to squash commits and do the merge.

Sorry I couldn't make the call today. Let me make a pass over the commits and take a gander. Is this PR good to go from your side otherwise?

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Here's what I propose:

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fnothaft commented Jan 4, 2017

Here's what I propose:

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Good plan, as long as we keep the commit message HTSJDK, gimme a break. 😖

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heuermh commented Jan 4, 2017

Good plan, as long as we keep the commit message HTSJDK, gimme a break. 😖

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@heuermh heuermh added this to the 0.21.0 milestone Jan 4, 2017

@fnothaft fnothaft referenced this pull request in Steven-N-Hart/VariantDB_Challenge Jan 5, 2017

Open

WIP ADAM queries. #6

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OK I will start squashing this on down.

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fnothaft commented Jan 5, 2017

OK I will start squashing this on down.

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Squashed and rebased.

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fnothaft commented Jan 5, 2017

Squashed and rebased.

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@heuermh heuermh merged commit 0a4a892 into bigdatagenomics:master Jan 5, 2017

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Thank you, @fnothaft @heuermh!

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heuermh commented Jan 5, 2017

Thank you, @fnothaft @heuermh!

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w00t! Thanks @heuermh for all the hard work getting this in!

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fnothaft commented Jan 5, 2017

w00t! Thanks @heuermh for all the hard work getting this in!

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Same to you!

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heuermh commented Jan 5, 2017

Same to you!

fnothaft added a commit to fnothaft/adam that referenced this pull request Jan 6, 2017

[ADAM-1342] Update CLI docs after #1288 merged.
Resolves #1342. Adds validation stringency documentation for vcf2adam and
adam2vcf. Removes mention of the anno2adam and flatten commands, which were
removed in #1288.

fnothaft added a commit to fnothaft/adam that referenced this pull request Jan 6, 2017

[ADAM-1342] Update CLI docs after #1288 merged.
Resolves #1342. Adds validation stringency documentation for vcf2adam and
adam2vcf. Removes mention of the anno2adam and flatten commands, which were
removed in #1288.

heuermh added a commit that referenced this pull request Jan 6, 2017

[ADAM-1342] Update CLI docs after #1288 merged.
Resolves #1342. Adds validation stringency documentation for vcf2adam and
adam2vcf. Removes mention of the anno2adam and flatten commands, which were
removed in #1288.
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