[ADAM-1424] Adding test for reads dropped in 0.21.0. #1448

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heuermh commented Mar 21, 2017

Fixes #1424.

Adapted unit test contributed by @xubo245 to use existing test resources.

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Coverage Status

Coverage increased (+0.2%) to 80.744% when pulling bf293cc on heuermh:issue-1424 into fd0cb6e on bigdatagenomics:master.

coveralls commented Mar 21, 2017

Coverage Status

Coverage increased (+0.2%) to 80.744% when pulling bf293cc on heuermh:issue-1424 into fd0cb6e 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/1894/

Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1448/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains bfcb1ef # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1448/merge^{commit} # timeout=10Checking out Revision bfcb1ef (origin/pr/1448/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f bfcb1eff43e621d34ccbeef519dfbf8399756238First 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 SUCCESSADAM-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 FAILUREADAM-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):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1894/

Build result: FAILURE

[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1448/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains bfcb1ef # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1448/merge^{commit} # timeout=10Checking out Revision bfcb1ef (origin/pr/1448/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f bfcb1eff43e621d34ccbeef519dfbf8399756238First 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 SUCCESSADAM-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 FAILUREADAM-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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heuermh commented Mar 21, 2017

Jenkins, retest this please.

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Coverage Status

Coverage increased (+0.2%) to 80.744% when pulling bf293cc on heuermh:issue-1424 into fd0cb6e on bigdatagenomics:master.

coveralls commented Mar 21, 2017

Coverage Status

Coverage increased (+0.2%) to 80.744% when pulling bf293cc on heuermh:issue-1424 into fd0cb6e on bigdatagenomics:master.

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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/1895/
Test PASSed.

Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1895/
Test PASSed.

@fnothaft fnothaft added this to the 0.22.0 milestone Mar 22, 2017

@@ -494,4 +494,15 @@ class ADAMContextSuite extends ADAMFunSuite {
case _ => fail("unexpected variant start " + v.getStart)
})
}
+
+ sparkTest("loadAlignments should not fail on single-end and paired-end fastq reads") {
+ val readsFilepath1 = testFile("proper_pairs_1.fq")

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OOC, does this test fail on 0.21.0?

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fnothaft Mar 22, 2017

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OOC, does this test fail on 0.21.0?

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Nope

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coveralls Mar 22, 2017

Coverage Status

Coverage increased (+0.1%) to 80.709% when pulling 2064adc on heuermh:issue-1424 into fd0cb6e on bigdatagenomics:master.

coveralls commented Mar 22, 2017

Coverage Status

Coverage increased (+0.1%) to 80.709% when pulling 2064adc on heuermh:issue-1424 into fd0cb6e on bigdatagenomics:master.

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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/1904/
Test PASSed.

Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1904/
Test PASSed.

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Squashed to a single commit

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heuermh commented Mar 22, 2017

Squashed to a single commit

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coveralls Mar 22, 2017

Coverage Status

Coverage increased (+0.2%) to 80.744% when pulling 1a436a6 on heuermh:issue-1424 into 629b778 on bigdatagenomics:master.

coveralls commented Mar 22, 2017

Coverage Status

Coverage increased (+0.2%) to 80.744% when pulling 1a436a6 on heuermh:issue-1424 into 629b778 on bigdatagenomics:master.

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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/1905/
Test PASSed.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1905/
Test PASSed.

@fnothaft fnothaft merged commit 65d8c9e into bigdatagenomics:master Mar 27, 2017

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codacy/pr Good work! A positive pull request.
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coverage/coveralls Coverage increased (+0.2%) to 80.744%
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default Merged build finished.
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@heuermh heuermh deleted the heuermh:issue-1424 branch Mar 27, 2017

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