Adding ReadRDD, SequenceRDD, and SliceRDD. #1895

heuermh · 2018-01-30T21:58:03Z

This pull request refactors NucleotideContigFragment to Sequence and Slice and adds new ADAMContext API methods:

// existing methods
def loadFastq(pathName: String, optPathName2: Option[String] = None, optRecordGroup: Option[String] = None, stringency: ValidationStringency = ValidationStringency.STRICT): AlignmentRecordDataset = {}

def loadPairedFastq(pathName1: String, pathName2: String, optRecordGroup: Option[String] = None, stringency: ValidationStringency = ValidationStringency.STRICT): AlignmentRecordDataset = {}

def loadUnpairedFastq(pathName: String, setFirstOfPair: Boolean = false, setSecondOfPair: Boolean = false, optRecordGroup: Option[String] = None, stringency: ValidationStringency = ValidationStringency.STRICT): AlignmentRecordDataset = {}

def loadInterleavedFastqAsFragments(pathName: String): FragmentDataset = {}

def loadPairedFastqAsFragments(pathName1: String, pathName2: String): FragmentDataset = {}

// new methods
def loadFastaDna(pathName: String): SequenceDataset = {}

def loadFastaProtein(pathName: String): SequenceDataset = {}

def loadFastaRna(pathName: String): SequenceDataset = {}

def loadFastaDna(pathName: String, maximumLength: Long = 10000L): SliceDataset = {}

def loadParquetReads(...): ReadDataset = {}

def loadParquetSequences(...): SequenceDataset = {}

def loadParquetSlices(...): SliceDataset = {}

def loadReads(pathName: String, optPredicate: Option[FilterPredicate], optProjection: Option[Schema] = None): ReadDataset = {}

def loadDnaSequences(pathName: String, optPredicate: Option[FilterPredicate], optProjection: Option[Schema] = None): SequenceDataset = {}

def loadProteinSequences(pathName: String, optPredicate: Option[FilterPredicate], optProjection: Option[Schema] = None): SequenceDataset = {}

def loadRnaSequences(pathName: String, optPredicate: Option[FilterPredicate], optProjection: Option[Schema] = None): SequenceDataset = {}

def loadSlices(pathName: String, maximumLength: Long = 10000L, optPredicate: Option[FilterPredicate], optProjection: Option[Schema] = None): SliceDataset = {}

External methods that extend ADAMContext

def loadGenbankDna(pathName: String): SequenceDataset = {}

def loadGenbankProtein(pathName: String): SequenceDataset = {}

def loadGenbankRna(pathName: String): SequenceDataset = {}

def loadGenbankDna(pathName: String, maximumLength: Long = 10000L): SliceDataset = {}

etc.

AmplabJenkins · 2018-01-30T22:26:31Z

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Build result: FAILURE

[...truncated 7 lines...] > /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 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 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/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 6055632 # timeout=10Checking out Revision 6055632 (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 6055632860706831bdf2c08ead110639ee1381daFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

coveralls · 2018-01-30T22:26:58Z

Coverage decreased (-3.4%) to 79.258% when pulling 3383a3c on heuermh:sequence-rdd-two into adff336 on bigdatagenomics:master.

coveralls · 2018-01-30T22:26:59Z

Coverage decreased (-3.4%) to 79.258% when pulling 3383a3c on heuermh:sequence-rdd-two into adff336 on bigdatagenomics:master.

coveralls · 2018-01-30T22:26:59Z

Coverage remained the same at ?% when pulling 5569f1e on heuermh:sequence-rdd-two into a512113 on bigdatagenomics:master.

coveralls · 2018-01-30T22:26:59Z

Coverage decreased (-3.4%) to 79.258% when pulling 3383a3c on heuermh:sequence-rdd-two into adff336 on bigdatagenomics:master.

AmplabJenkins · 2018-01-31T02:26:09Z

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[...truncated 7 lines...] > /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 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 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/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 723d1cf # timeout=10Checking out Revision 723d1cf (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 723d1cf855c29160ec818e3995e1e08984f60319First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
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AmplabJenkins · 2018-01-31T03:01:04Z

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AmplabJenkins · 2018-02-02T21:22:44Z

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[...truncated 7 lines...] > /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 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 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/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 70594c6 # timeout=10Checking out Revision 70594c6 (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 70594c69954117a0b0f479803d9042fd26a1e067First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2018-02-04T00:19:10Z

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[...truncated 7 lines...] > /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 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 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/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 3fccb8f # timeout=10Checking out Revision 3fccb8f (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 3fccb8f27e0a59f77df4597277bac891fc852148First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2018-02-07T19:54:54Z

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[...truncated 7 lines...] > /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 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 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/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 74766f0 # timeout=10Checking out Revision 74766f0 (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 74766f0375c433ff60fa5dc296336f6bf91f1996First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

antonkulaga · 2018-02-10T22:58:59Z

Is it the PR that should solve my FastConverter problems?

heuermh · 2018-02-10T23:04:46Z

Is it the PR that should solve my FastConverter problems?

That is the intent; it doesn't yet. It does allow for https://github.com/heuermh/biojava-adam as a workaround. I will run some performance comparisons on our cluster on Monday.

AmplabJenkins · 2018-02-14T00:52:46Z

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Build result: FAILURE

[...truncated 7 lines...] > /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 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 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/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 93a07ac # timeout=10Checking out Revision 93a07ac (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 93a07ac9bd72d891152c1a38b18851af66553f88First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2018-03-05T18:36:31Z

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Build result: FAILURE

[...truncated 7 lines...] > /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 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 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/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 0a4e4d6 # timeout=10Checking out Revision 0a4e4d6 (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 0a4e4d6849da43ca07dab1933a15f5a390bbab81First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

antonkulaga · 2018-04-12T22:51:35Z

I do not see this very important issue in the roadmap for 0.25, do you want to release it later?

heuermh · 2018-04-12T23:08:20Z

Sorry, as evident from all the conflicting files, this is a large change and is sensitive to further refactoring. #1981 is another large one that needs to go first. I'd like to have this in 0.25.0, which has a due date of May 1st.

AmplabJenkins · 2018-04-25T19:05:48Z

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[...truncated 7 lines...] > /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 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 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/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 646b91f # timeout=10Checking out Revision 646b91f (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 646b91f44a78729620c138f1407d5ab20b02e93aFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2018-05-01T23:38:39Z

Test FAILed.
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Build result: ABORTED

[...truncated 7 lines...] > /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 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 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/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 4a8e4fb # timeout=10Checking out Revision 4a8e4fb (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 4a8e4fb45e86a4deb6db2a5a4b5f1c64e36cd9ddFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result ABORTEDADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2018-05-06T20:58:58Z

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

[...truncated 7 lines...] > /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 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 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/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 9a88e8d # timeout=10Checking out Revision 9a88e8d (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 9a88e8dc1d05545b87a37946cc6a0da7f1c8ce21First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2018-05-06T21:35:30Z

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

[...truncated 7 lines...] > /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 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 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/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains d163c58 # timeout=10Checking out Revision d163c58 (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f d163c58a08ab92c6df4df83823e9fa1c9ae635b3First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2018-05-07T20:29:15Z

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

[...truncated 7 lines...] > /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 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 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/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 454da56 # timeout=10Checking out Revision 454da56 (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 454da56226d67ffced14877bff56c14d60f298caFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2018-05-07T21:25:44Z

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

[...truncated 7 lines...] > /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 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 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/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 7c91b67 # timeout=10Checking out Revision 7c91b67 (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 7c91b67e9eb492e041874713dc96c371bd8ca599First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2019-05-31T17:01:48Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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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 > git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/1895/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 8af6dc8 # timeout=10Checking out Revision 8af6dc8 (origin/pr/1895/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 8af6dc861fe260eddb48c29fbcdb28dc949600c3First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.12,2.4.3,ubuntuTriggering ADAM-prb ? 2.7.5,2.11,2.4.3,ubuntuADAM-prb ? 2.7.5,2.12,2.4.3,ubuntu completed with result FAILUREADAM-prb ? 2.7.5,2.11,2.4.3,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2019-05-31T20:54:57Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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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 > git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/1895/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains c704f75 # timeout=10Checking out Revision c704f75 (origin/pr/1895/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f c704f758054ede1f9ca952c476db5c94a05e4ae8First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.12,2.4.3,ubuntuTriggering ADAM-prb ? 2.7.5,2.11,2.4.3,ubuntuADAM-prb ? 2.7.5,2.12,2.4.3,ubuntu completed with result FAILUREADAM-prb ? 2.7.5,2.11,2.4.3,ubuntu completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2019-05-31T22:18:09Z

Test PASSed.
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Test PASSed.

AmplabJenkins · 2019-06-01T00:47:40Z

Test PASSed.
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Test PASSed.

AmplabJenkins · 2019-06-01T04:03:31Z

Test PASSed.
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Test PASSed.

AmplabJenkins · 2019-06-02T20:18:56Z

Test PASSed.
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Test PASSed.

AmplabJenkins · 2019-06-02T20:19:16Z

Test FAILed.
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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 > git init /home/jenkins/workspace/ADAM-prb # 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/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/1895/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains cbf94f1 # timeout=10Checking out Revision cbf94f1 (origin/pr/1895/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f cbf94f13d2a14bd5795aaaffdf3187213beb62caFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.12,2.4.3,ubuntuTriggering ADAM-prb ? 2.7.5,2.11,2.4.3,ubuntuADAM-prb ? 2.7.5,2.12,2.4.3,ubuntu completed with result FAILUREADAM-prb ? 2.7.5,2.11,2.4.3,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2019-06-02T21:04:01Z

Test PASSed.
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Test PASSed.

antonkulaga · 2019-06-04T09:08:12Z

Hope it will be merged soon, waiting 4 hours just to load new mouse transcriptome from the fasta file is killing me!

heuermh · 2019-06-05T15:33:17Z

@antonkulaga Yes, I hope to get this merged this week, it has been sitting around for far too long.

heuermh mentioned this pull request Jan 30, 2018

Adding read, sequence, and slice RDDs #1505

Closed

heuermh force-pushed the sequence-rdd-two branch from 460f6bf to 12285a1 Compare February 2, 2018 20:49

heuermh force-pushed the sequence-rdd-two branch from 12285a1 to 1ea3984 Compare February 3, 2018 23:50

heuermh force-pushed the sequence-rdd-two branch from 1ea3984 to e381016 Compare February 7, 2018 18:21

heuermh force-pushed the sequence-rdd-two branch from e381016 to 50c34ae Compare February 14, 2018 00:23

heuermh force-pushed the sequence-rdd-two branch from 50c34ae to cb0ba2f Compare March 5, 2018 18:02

heuermh force-pushed the sequence-rdd-two branch from cb0ba2f to ee44ce1 Compare April 25, 2018 18:34

heuermh added this to the 0.28.0 milestone May 7, 2019

heuermh force-pushed the sequence-rdd-two branch from 38cb59c to e6a045d Compare May 31, 2019 16:27

heuermh mentioned this pull request May 31, 2019

Code generate conversion functions from templates #2163

Closed

heuermh force-pushed the sequence-rdd-two branch from bffd771 to a785087 Compare May 31, 2019 23:57

heuermh requested a review from akmorrow13 June 1, 2019 00:48

Adding ReadRDD, SequenceRDD, and SliceRDD.

5569f1e

heuermh force-pushed the sequence-rdd-two branch from bd3d08c to 5569f1e Compare June 2, 2019 20:14

heuermh mentioned this pull request Jun 6, 2019

Add SAM record converters, VCF record converter API classes bigdatagenomics/convert#71

Merged

heuermh merged commit 38973ae into bigdatagenomics:master Jun 12, 2019

heuermh deleted the sequence-rdd-two branch June 12, 2019 17:06

heuermh mentioned this pull request Jun 13, 2019

Should NucleotideContigFragmentRDD create sequence dictionary on load? #1894

Closed

heuermh mentioned this pull request Jun 29, 2019

Improve unit test coverage for NucleotideContigFragmentRDD #1413

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Adding ReadRDD, SequenceRDD, and SliceRDD. #1895

Adding ReadRDD, SequenceRDD, and SliceRDD. #1895

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Adding ReadRDD, SequenceRDD, and SliceRDD. #1895

Adding ReadRDD, SequenceRDD, and SliceRDD. #1895

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Build result: FAILURE

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AmplabJenkins commented Apr 25, 2018

Build result: FAILURE

AmplabJenkins commented May 1, 2018

Build result: ABORTED

AmplabJenkins commented May 6, 2018

Build result: FAILURE

AmplabJenkins commented May 6, 2018

Build result: FAILURE

AmplabJenkins commented May 7, 2018

Build result: FAILURE

AmplabJenkins commented May 7, 2018

Build result: FAILURE

AmplabJenkins commented May 31, 2019

Build result: FAILURE

AmplabJenkins commented May 31, 2019

Build result: FAILURE

AmplabJenkins commented May 31, 2019

AmplabJenkins commented Jun 1, 2019

AmplabJenkins commented Jun 1, 2019

AmplabJenkins commented Jun 2, 2019

AmplabJenkins commented Jun 2, 2019

Build result: FAILURE

AmplabJenkins commented Jun 2, 2019

antonkulaga commented Jun 4, 2019

heuermh commented Jun 5, 2019

heuermh commented Jan 30, 2018 •

edited

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coveralls commented Jan 30, 2018 •

edited

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heuermh commented Apr 12, 2018 •

edited

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