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added JavaApi for loadCoverage #1437

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merged 1 commit into from Mar 15, 2017

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akmorrow13 commented Mar 14, 2017

Resolves #1420

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Coverage Status

Coverage decreased (-0.05%) to 76.611% when pulling edfe707 on akmorrow13:javaApi into b8477dc on bigdatagenomics:master.

coveralls commented Mar 14, 2017

Coverage Status

Coverage decreased (-0.05%) to 76.611% when pulling edfe707 on akmorrow13:javaApi into b8477dc on bigdatagenomics:master.

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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/1867/

Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1437/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 722171a62e5d70e7037012970dcc600a1ed5550d # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1437/merge^{commit} # timeout=10Checking out Revision 722171a62e5d70e7037012970dcc600a1ed5550d (origin/pr/1437/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 722171a62e5d70e7037012970dcc600a1ed5550dFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSNotifying 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):
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Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1437/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 722171a62e5d70e7037012970dcc600a1ed5550d # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1437/merge^{commit} # timeout=10Checking out Revision 722171a62e5d70e7037012970dcc600a1ed5550d (origin/pr/1437/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 722171a62e5d70e7037012970dcc600a1ed5550dFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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Jenkins, retest this please.

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fnothaft commented Mar 14, 2017

Jenkins, retest this please.

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akmorrow13 Mar 14, 2017

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Adding tests.

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akmorrow13 commented Mar 14, 2017

Adding tests.

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Jenkins, retest this please.

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akmorrow13 commented Mar 14, 2017

Jenkins, retest this please.

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Coverage Status

Coverage decreased (-0.03%) to 76.628% when pulling 824acd3 on akmorrow13:javaApi into b8477dc on bigdatagenomics:master.

coveralls commented Mar 14, 2017

Coverage Status

Coverage decreased (-0.03%) to 76.628% when pulling 824acd3 on akmorrow13:javaApi into b8477dc on bigdatagenomics:master.

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Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1870/
Test PASSed.

Test PASSed.
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Test PASSed.

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Coverage Status

Coverage decreased (-0.03%) to 76.628% when pulling 824acd3 on akmorrow13:javaApi into b8477dc on bigdatagenomics:master.

coveralls commented Mar 14, 2017

Coverage Status

Coverage decreased (-0.03%) to 76.628% when pulling 824acd3 on akmorrow13:javaApi into b8477dc on bigdatagenomics:master.

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Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1871/
Test PASSed.

Test PASSed.
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Test PASSed.

Show outdated Hide outdated ...-apis/src/main/scala/org/bdgenomics/adam/apis/java/JavaADAMContext.scala
@@ -84,6 +84,16 @@ class JavaADAMContext(val ac: ADAMContext) extends Serializable {
}
/**
* Loads in a coverage file. This method can load BED, NARROWPEAK, and ADAM files.

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NARROWPEAK → NarrowPeak as used elsewhere

What about the other feature formats (i.e. GFF3, GTF/GFF2, and IntervalList) supported by loadFeatures?

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NARROWPEAK → NarrowPeak as used elsewhere

What about the other feature formats (i.e. GFF3, GTF/GFF2, and IntervalList) supported by loadFeatures?

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Coverage Status

Coverage increased (+0.07%) to 76.628% when pulling 83e64b1 on akmorrow13:javaApi into 9938d3c on bigdatagenomics:master.

coveralls commented Mar 14, 2017

Coverage Status

Coverage increased (+0.07%) to 76.628% when pulling 83e64b1 on akmorrow13:javaApi into 9938d3c on bigdatagenomics:master.

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Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1876/
Test PASSed.

Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1876/
Test PASSed.

@heuermh heuermh merged commit cf39e6c into bigdatagenomics:master Mar 15, 2017

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coverage/coveralls Coverage increased (+0.07%) to 76.628%
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Thank you, @akmorrow13!

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heuermh commented Mar 15, 2017

Thank you, @akmorrow13!

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