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Upgrade to bdg-formats:0.6.0, add Fragment datatype converters #815

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fnothaft commented Aug 28, 2015

Resolves #779, #788. This is a fairly big PR and could use some close review. I'm CCing @arahuja to review the modifications to the VariantContextConverter, and @laserson and @ilveroluca to review the Fragment additions.

There are a few things in specific that I think could use a closer look. I'll comment on these inline.

@@ -39,6 +46,12 @@ object PhredUtils {
def errorProbabilityToPhred(p: Double): Int = probabilityToPhred(p)
def logProbabilityToPhred(p: Float): Int = if (p == 0.0) {
256

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This clips us to max probability if we saturate.

@fnothaft

fnothaft Aug 28, 2015

Member

This clips us to max probability if we saturate.

assert(adamGT1.getGenotypeLikelihoods
.map(f => f: scala.Float)
.map(PhredUtils.logProbabilityToPhred)
.sameElements(List(59, 0, 256)))

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Previously, since we were going Phred to Phred, we had enough precision to express this. Going Phred to log probabilities, we seem to clip around 1-1e13. Does anyone think this is a problem? I personally don't think it makes sense to worry much about the sensitivity of probabilities that are asymptotically close to 1.0.

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Previously, since we were going Phred to Phred, we had enough precision to express this. Going Phred to log probabilities, we seem to clip around 1-1e13. Does anyone think this is a problem? I personally don't think it makes sense to worry much about the sensitivity of probabilities that are asymptotically close to 1.0.

@@ -265,21 +275,21 @@ class VariantContextConverter(dict: Option[SequenceDictionary] = None) extends S
assert(vc.isBiallelic)
extractGenotypes(vc, variant, annotations,
(g: htsjdk.variant.variantcontext.Genotype, b: Genotype.Builder) => {
if (g.hasPL) b.setGenotypeLikelihoods(g.getPL.toList.map(p => p: java.lang.Integer))
if (g.hasPL) b.setGenotypeLikelihoods(g.getPL.toList.map(p => jFloat(PhredUtils.phredToLogProbability(p))))

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@arahuja On bigdatagenomics/bdg-formats#51, we agreed to move to log probabilities. We were moving to log success probabilities, correct? This is written for log success probabilities, not log error probabilities.

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fnothaft Aug 28, 2015

Member

@arahuja On bigdatagenomics/bdg-formats#51, we agreed to move to log probabilities. We were moving to log success probabilities, correct? This is written for log success probabilities, not log error probabilities.

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arahuja Sep 9, 2015

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Yes, I was assuming success probabilities

@arahuja

arahuja Sep 9, 2015

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Yes, I was assuming success probabilities

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fnothaft Sep 9, 2015

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OK, great!

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fnothaft Sep 9, 2015

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OK, great!

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GitHub pull request #815 of commit fb9d61b 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/815/merge^{commit} # timeout=10 > git branch -a --contains 4f6bb9dd5981f6a3e9f3d9a8603fceea97ba47c3 # timeout=10 > git rev-parse remotes/origin/pr/815/merge^{commit} # timeout=10Checking out Revision 4f6bb9dd5981f6a3e9f3d9a8603fceea97ba47c3 (origin/pr/815/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 4f6bb9dd5981f6a3e9f3d9a8603fceea97ba47c3First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,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 #815 of commit fb9d61b 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/815/merge^{commit} # timeout=10 > git branch -a --contains 4f6bb9dd5981f6a3e9f3d9a8603fceea97ba47c3 # timeout=10 > git rev-parse remotes/origin/pr/815/merge^{commit} # timeout=10Checking out Revision 4f6bb9dd5981f6a3e9f3d9a8603fceea97ba47c3 (origin/pr/815/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 4f6bb9dd5981f6a3e9f3d9a8603fceea97ba47c3First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,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 #815 of commit f748972 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/815/merge^{commit} # timeout=10 > git branch -a --contains 2652b76 # timeout=10 > git rev-parse remotes/origin/pr/815/merge^{commit} # timeout=10Checking out Revision 2652b76 (origin/pr/815/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 2652b76de6cc2f4a8f71ba26634cac6f5db01bd6First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,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 #815 of commit f748972 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/815/merge^{commit} # timeout=10 > git branch -a --contains 2652b76 # timeout=10 > git rev-parse remotes/origin/pr/815/merge^{commit} # timeout=10Checking out Revision 2652b76 (origin/pr/815/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 2652b76de6cc2f4a8f71ba26634cac6f5db01bd6First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@@ -74,16 +77,52 @@ class FastqRecordConverter extends Serializable with Logging {
.build())
}
def convertFragment(element: (Void, Text)): Fragment = {
val lines = element._2.toString.split('\n')
require(lines.length == 8, "Record has wrong format:\n" + element._2.toString)

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heuermh Aug 28, 2015

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I don't believe this is a fair assumption, and is most likely also a problem with FASTQ processing in ADAM generally.

Have a look at some pathological cases here
https://github.com/biojava/biojava/tree/master/biojava-sequencing/src/test/resources/org/biojava/nbio/sequencing/io/fastq

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heuermh Aug 28, 2015

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I don't believe this is a fair assumption, and is most likely also a problem with FASTQ processing in ADAM generally.

Have a look at some pathological cases here
https://github.com/biojava/biojava/tree/master/biojava-sequencing/src/test/resources/org/biojava/nbio/sequencing/io/fastq

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fnothaft Aug 28, 2015

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I agree. However, there's a fairly long history to this problem. If you want to track back through it, I might start with PR #679. I think we should fix the FASTQ record parser to support the full FASTQ spec, but it is a low priority from my perspective, which is really just me saying that no one has come to me/the list screaming about it.

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fnothaft Aug 28, 2015

Member

I agree. However, there's a fairly long history to this problem. If you want to track back through it, I might start with PR #679. I think we should fix the FASTQ record parser to support the full FASTQ spec, but it is a low priority from my perspective, which is really just me saying that no one has come to me/the list screaming about it.

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heuermh Sep 22, 2015

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ok I'll let this go for now

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heuermh Sep 22, 2015

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ok I'll let this go for now

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Jenkins, test this please.

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massie commented Sep 8, 2015

Jenkins, test this please.

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Build result: FAILURE

GitHub pull request #815 of commit f748972 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/815/merge^{commit} # timeout=10 > git branch -a --contains 2652b76 # timeout=10 > git rev-parse remotes/origin/pr/815/merge^{commit} # timeout=10Checking out Revision 2652b76 (origin/pr/815/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 2652b76de6cc2f4a8f71ba26634cac6f5db01bd6First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,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 #815 of commit f748972 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/815/merge^{commit} # timeout=10 > git branch -a --contains 2652b76 # timeout=10 > git rev-parse remotes/origin/pr/815/merge^{commit} # timeout=10Checking out Revision 2652b76 (origin/pr/815/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 2652b76de6cc2f4a8f71ba26634cac6f5db01bd6First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

getFilter(0x40, _.getFirstOfPair),
getFilter(0x80, _.getSecondOfPair),
getFilter(0x40, _.getReadNum == 0),
getFilter(0x80, _.getReadNum == 1),

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massie Sep 8, 2015

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This isn't related to this PR. I think the name getReadNum needs to be clarified. When I first saw it, I thought it was a unique ID per read (and went to look at the source for how we implemented it). Maybe getFragmentReadNumber or somesuch name will make it clearer. Nothing to change for this PR.

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This isn't related to this PR. I think the name getReadNum needs to be clarified. When I first saw it, I thought it was a unique ID per read (and went to look at the source for how we implemented it). Maybe getFragmentReadNumber or somesuch name will make it clearer. Nothing to change for this PR.

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fnothaft Sep 8, 2015

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I've opened bigdatagenomics/bdg-formats#62 for this.

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fnothaft Sep 8, 2015

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I've opened bigdatagenomics/bdg-formats#62 for this.

"2"
)
adamRecord.getReadPaired) {
"/%d".format(adamRecord.getReadNum + 1)
} else {
""
}

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Just below here, when we create the qualityScores string, e.g.

val qualityScores =
       if (outputOriginalBaseQualities && adamRecord.getOrigQual != null)
         adamRecord.getOrigQual
       else
         adamRecord.getQual

We need to update this to be changed I think. If a user requests the original quality scores, and they don't exist, they will be get the updated scores without as much as an error.

Something like, e.g.

val qualityScores =
      if (outputOriginalBaseQualities)
        Option(adamRecord.getOrigQual).getOrElse("*")
      else
        adamRecord.getQual

would be better.

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massie Sep 8, 2015

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Just below here, when we create the qualityScores string, e.g.

val qualityScores =
       if (outputOriginalBaseQualities && adamRecord.getOrigQual != null)
         adamRecord.getOrigQual
       else
         adamRecord.getQual

We need to update this to be changed I think. If a user requests the original quality scores, and they don't exist, they will be get the updated scores without as much as an error.

Something like, e.g.

val qualityScores =
      if (outputOriginalBaseQualities)
        Option(adamRecord.getOrigQual).getOrElse("*")
      else
        adamRecord.getQual

would be better.

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fnothaft Sep 8, 2015

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I think this could use more discussion, so I've opened #818.

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fnothaft Sep 8, 2015

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I think this could use more discussion, so I've opened #818.

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What the advantage of having the discussion on #818 instead of in this PR? Just curious.

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massie Sep 8, 2015

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What the advantage of having the discussion on #818 instead of in this PR? Just curious.

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The quality score code isn't changed by this PR, so I'd prefer to have modifications to resolve #818 come in as a separate change. Additionally, since this is a pretty big PR already, I thought it'd be a bit easier to follow if side issues were tracked in separate tickets.

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The quality score code isn't changed by this PR, so I'd prefer to have modifications to resolve #818 come in as a separate change. Additionally, since this is a pretty big PR already, I thought it'd be a bit easier to follow if side issues were tracked in separate tickets.

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massie Sep 9, 2015

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Fair enough.

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massie Sep 9, 2015

Member

Fair enough.

@@ -26,7 +26,11 @@ import htsjdk.variant.variantcontext.{
}
import java.util.Collections
import org.apache.spark.Logging
import org.bdgenomics.adam.models.{ VariantContext => ADAMVariantContext, SequenceDictionary }
import org.bdgenomics.adam.models.{

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massie Sep 8, 2015

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This can all be on a single line.

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massie Sep 8, 2015

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This can all be on a single line.

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As a single line, this would be 94 characters. Since that is >80, I split the line.

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fnothaft Sep 8, 2015

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As a single line, this would be 94 characters. Since that is >80, I split the line.

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heuermh Sep 8, 2015

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for what it's worth, I'd be ok bumping the line width in the formatter to 120 characters :)

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heuermh Sep 8, 2015

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for what it's worth, I'd be ok bumping the line width in the formatter to 120 characters :)

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I personally prefer < 80 as I am frequently programming on a split screen on a laptop.

I don't think this is one of those conversations that historically ends well... ;)

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fnothaft Sep 8, 2015

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I personally prefer < 80 as I am frequently programming on a split screen on a laptop.

I don't think this is one of those conversations that historically ends well... ;)

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[...truncated 16 lines...]First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.3.1,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 ? 2.3.0,2.11,1.2.1,centosTriggering ADAM-prb ? 1.0.4,2.11,1.2.1,centosTriggering ADAM-prb ? 1.0.4,2.10,1.2.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.2.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.3.1,centosADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result FAILUREADAM-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 FAILUREADAM-prb ? 2.3.0,2.11,1.2.1,centos completed with result FAILUREADAM-prb ? 1.0.4,2.11,1.2.1,centos completed with result FAILUREADAM-prb ? 1.0.4,2.10,1.2.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.2.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
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Build result: FAILURE

[...truncated 16 lines...]First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.3.1,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 ? 2.3.0,2.11,1.2.1,centosTriggering ADAM-prb ? 1.0.4,2.11,1.2.1,centosTriggering ADAM-prb ? 1.0.4,2.10,1.2.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.2.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.3.1,centosADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result FAILUREADAM-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 FAILUREADAM-prb ? 2.3.0,2.11,1.2.1,centos completed with result FAILUREADAM-prb ? 1.0.4,2.11,1.2.1,centos completed with result FAILUREADAM-prb ? 1.0.4,2.10,1.2.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.2.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Build result: FAILURE

[...truncated 16 lines...]First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.3.1,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 ? 2.3.0,2.11,1.2.1,centosTriggering ADAM-prb ? 1.0.4,2.11,1.2.1,centosTriggering ADAM-prb ? 1.0.4,2.10,1.2.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.2.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.3.1,centosADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result FAILUREADAM-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 FAILUREADAM-prb ? 2.3.0,2.11,1.2.1,centos completed with result FAILUREADAM-prb ? 1.0.4,2.11,1.2.1,centos completed with result FAILUREADAM-prb ? 1.0.4,2.10,1.2.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.2.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Build result: FAILURE

[...truncated 16 lines...]First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.3.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.3.1,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 ? 2.3.0,2.11,1.2.1,centosTriggering ADAM-prb ? 1.0.4,2.11,1.2.1,centosTriggering ADAM-prb ? 1.0.4,2.10,1.2.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.2.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.3.1,centosADAM-prb ? 2.3.0,2.10,1.3.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.3.1,centos completed with result FAILUREADAM-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 FAILUREADAM-prb ? 2.3.0,2.11,1.2.1,centos completed with result FAILUREADAM-prb ? 1.0.4,2.11,1.2.1,centos completed with result FAILUREADAM-prb ? 1.0.4,2.10,1.2.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.4.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.2.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.3.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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oops

[ERROR] Failed to execute goal on project adam-core_2.10: Could not resolve dependencies for project org.bdgenomics.adam:adam-core_2.10:jar:0.17.2-SNAPSHOT: Could not find artifact org.bdgenomics.bdg-formats:bdg-formats:jar:e1ca0a3 in central (http://repo.maven.apache.org/maven2) -> [Help 1]

fnothaft#7 was merged in here but was still pointing to a custom build of bdg-formats later than 0.6.0

Let me push my change to bdg-formats, we can release a 0.6.1 or 0.7.0, then depend on that here.

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ryan-williams commented Sep 21, 2015

oops

[ERROR] Failed to execute goal on project adam-core_2.10: Could not resolve dependencies for project org.bdgenomics.adam:adam-core_2.10:jar:0.17.2-SNAPSHOT: Could not find artifact org.bdgenomics.bdg-formats:bdg-formats:jar:e1ca0a3 in central (http://repo.maven.apache.org/maven2) -> [Help 1]

fnothaft#7 was merged in here but was still pointing to a custom build of bdg-formats later than 0.6.0

Let me push my change to bdg-formats, we can release a 0.6.1 or 0.7.0, then depend on that here.

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Proposed bigdatagenomics/bdg-formats#63 with the change that fnothaft#7 (and now this PR) needs

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ryan-williams commented Sep 21, 2015

Proposed bigdatagenomics/bdg-formats#63 with the change that fnothaft#7 (and now this PR) needs

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This is up to date with @ryan-williams's fixes (that upgrade us to bdg-formats/0.6.1). I think this resolves all outstanding issues.

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fnothaft commented Sep 22, 2015

This is up to date with @ryan-williams's fixes (that upgrade us to bdg-formats/0.6.1). I think this resolves all outstanding issues.

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Test FAILed.
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Build result: FAILURE

GitHub pull request #815 of commit d2e9478 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/815/merge^{commit} # timeout=10 > git branch -a --contains bc4503d59d30134ccbdc82c62e6fbadc43b86677 # timeout=10 > git rev-parse remotes/origin/pr/815/merge^{commit} # timeout=10Checking out Revision bc4503d59d30134ccbdc82c62e6fbadc43b86677 (origin/pr/815/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f bc4503d59d30134ccbdc82c62e6fbadc43b86677 > git rev-list 74212d3177a2a30e9ea6ae30306ae2c08c26a5cc # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,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 #815 of commit d2e9478 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/815/merge^{commit} # timeout=10 > git branch -a --contains bc4503d59d30134ccbdc82c62e6fbadc43b86677 # timeout=10 > git rev-parse remotes/origin/pr/815/merge^{commit} # timeout=10Checking out Revision bc4503d59d30134ccbdc82c62e6fbadc43b86677 (origin/pr/815/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f bc4503d59d30134ccbdc82c62e6fbadc43b86677 > git rev-list 74212d3177a2a30e9ea6ae30306ae2c08c26a5cc # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,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 Sep 22, 2015

Jenkins, test this please.

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Test FAILed.
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Build result: FAILURE

GitHub pull request #815 of commit d2e9478 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/815/merge^{commit} # timeout=10 > git branch -a --contains bc4503d59d30134ccbdc82c62e6fbadc43b86677 # timeout=10 > git rev-parse remotes/origin/pr/815/merge^{commit} # timeout=10Checking out Revision bc4503d59d30134ccbdc82c62e6fbadc43b86677 (origin/pr/815/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f bc4503d59d30134ccbdc82c62e6fbadc43b86677 > git rev-list bc4503d59d30134ccbdc82c62e6fbadc43b86677 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,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 #815 of commit d2e9478 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/815/merge^{commit} # timeout=10 > git branch -a --contains bc4503d59d30134ccbdc82c62e6fbadc43b86677 # timeout=10 > git rev-parse remotes/origin/pr/815/merge^{commit} # timeout=10Checking out Revision bc4503d59d30134ccbdc82c62e6fbadc43b86677 (origin/pr/815/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f bc4503d59d30134ccbdc82c62e6fbadc43b86677 > git rev-list bc4503d59d30134ccbdc82c62e6fbadc43b86677 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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missing unordered.sam, maybe I forgot to git add it?

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ryan-williams commented Sep 22, 2015

missing unordered.sam, maybe I forgot to git add it?

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or it's in adam-core test/resources and is being referenced from adam-cli and the latter's not finding it

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ryan-williams commented Sep 22, 2015

or it's in adam-core test/resources and is being referenced from adam-cli and the latter's not finding it

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Ah, let me fix that.

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fnothaft commented Sep 22, 2015

Ah, let me fix that.

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weirdly, it passes for me locally.

should we make adam-cli tests include the adam-core test/resources in their resources path?

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ryan-williams commented Sep 22, 2015

weirdly, it passes for me locally.

should we make adam-cli tests include the adam-core test/resources in their resources path?

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we already do a somewhat silly thing and have the same bqsr1.sam file in adam-cli and adam-core

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ryan-williams commented Sep 22, 2015

we already do a somewhat silly thing and have the same bqsr1.sam file in adam-cli and adam-core

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Yeah, I've just symlinked them from adam-core to adam-cli.

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fnothaft commented Sep 22, 2015

Yeah, I've just symlinked them from adam-core to adam-cli.

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Build result: FAILURE

GitHub pull request #815 of commit 9307008 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/815/merge^{commit} # timeout=10 > git branch -a --contains b78391d # timeout=10 > git rev-parse remotes/origin/pr/815/merge^{commit} # timeout=10Checking out Revision b78391d (origin/pr/815/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f b78391d > git rev-list bc4503d59d30134ccbdc82c62e6fbadc43b86677 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,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 #815 of commit 9307008 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/815/merge^{commit} # timeout=10 > git branch -a --contains b78391d # timeout=10 > git rev-parse remotes/origin/pr/815/merge^{commit} # timeout=10Checking out Revision b78391d (origin/pr/815/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f b78391d > git rev-list bc4503d59d30134ccbdc82c62e6fbadc43b86677 # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,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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ryan-williams commented Sep 22, 2015

Jenkins, retest this please

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Test PASSed.

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Test PASSed.

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Could we get merge/additional review by the end of the week? This has been open more than a month.

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fnothaft commented Sep 28, 2015

Could we get merge/additional review by the end of the week? This has been open more than a month.

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This LGTM @fnothaft. A couple of observations:

  • Sorry that my PR on this PR has cluttered up the review here! I think that leaving that one hanging until we got this one in might have been a better course of action, I'll try to be more clear about that in the future.
  • This seems similar to the last time I looked at it but with the simplification that you took out the Sequence stuff and just have ARs in the Fragment, right?
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ryan-williams commented Sep 28, 2015

This LGTM @fnothaft. A couple of observations:

  • Sorry that my PR on this PR has cluttered up the review here! I think that leaving that one hanging until we got this one in might have been a better course of action, I'll try to be more clear about that in the future.
  • This seems similar to the last time I looked at it but with the simplification that you took out the Sequence stuff and just have ARs in the Fragment, right?

erictu and others added some commits Aug 19, 2015

[ADAM-788] Adds conversion code for Fragments.
Fragments are similar to the SingleReadBucket and describe reads generated from
a single fragment of DNA. This commit adds the following:

- Conversion code from AlignmentRecords to Fragments, and vice versa.
- Conversion code for going directly from interleaved FASTQ to Fragments.
- CLI code for importing fragments.
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Fixed the oops @ryan-williams and rebased.

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fnothaft commented Sep 29, 2015

Fixed the oops @ryan-williams and rebased.

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https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/946/

Build result: FAILURE

GitHub pull request #815 of commit 283ea9d 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/815/merge^{commit} # timeout=10 > git branch -a --contains 3506f59eec4f134e457c43afa5dd771bb1eaec03 # timeout=10 > git rev-parse remotes/origin/pr/815/merge^{commit} # timeout=10Checking out Revision 3506f59eec4f134e457c43afa5dd771bb1eaec03 (origin/pr/815/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3506f59eec4f134e457c43afa5dd771bb1eaec03 > git rev-list b78391d # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins commented Sep 29, 2015

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/946/

Build result: FAILURE

GitHub pull request #815 of commit 283ea9d 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/815/merge^{commit} # timeout=10 > git branch -a --contains 3506f59eec4f134e457c43afa5dd771bb1eaec03 # timeout=10 > git rev-parse remotes/origin/pr/815/merge^{commit} # timeout=10Checking out Revision 3506f59eec4f134e457c43afa5dd771bb1eaec03 (origin/pr/815/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3506f59eec4f134e457c43afa5dd771bb1eaec03 > git rev-list b78391d # timeout=10Triggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,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 Sep 29, 2015

Jenkins, test 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/948/
Test PASSed.

AmplabJenkins commented Sep 29, 2015

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/948/
Test PASSed.

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@massie @laserson @ryan-williams if I don't get any further comments on this, I will merge it myself on Monday.

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fnothaft commented Oct 1, 2015

@massie @laserson @ryan-williams if I don't get any further comments on this, I will merge it myself on Monday.

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I just reviewed this again and I didn't see any outstanding issues by @laserson or @ryan-williams, so I'm going to merge it now.

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massie commented Oct 1, 2015

I just reviewed this again and I didn't see any outstanding issues by @laserson or @ryan-williams, so I'm going to merge it now.

@massie massie merged commit 283ea9d into bigdatagenomics:master Oct 1, 2015

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