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Update load method docs in Python and R. #1619

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merged 1 commit into from Jul 21, 2017

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@heuermh
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@heuermh heuermh commented Jul 21, 2017

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@coveralls coveralls commented Jul 21, 2017

Coverage Status

Coverage increased (+0.5%) to 84.743% when pulling 65a3c44 on heuermh:load-docs into 640c44b on bigdatagenomics:master.

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@AmplabJenkins AmplabJenkins commented Jul 21, 2017

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2258/

Build result: FAILURE

[...truncated 15 lines...] > /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/1619/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 4ce56d28bceb32561d8624f71e4d0694c38c4bf3 # timeout=10Checking out Revision 4ce56d28bceb32561d8624f71e4d0694c38c4bf3 (origin/pr/1619/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 4ce56d28bceb32561d8624f71e4d0694c38c4bf3First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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@AmplabJenkins AmplabJenkins commented Jul 21, 2017

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2259/

Build result: FAILURE

[...truncated 15 lines...] > /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/1619/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 28082a5 # timeout=10Checking out Revision 28082a5 (origin/pr/1619/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 28082a51d6ccebf0e805edc8c4d5fa9681480ef7First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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@heuermh heuermh commented Jul 21, 2017

Jenkins, retest this please.

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@coveralls coveralls commented Jul 21, 2017

Coverage Status

Coverage increased (+0.5%) to 84.743% when pulling 65a3c44 on heuermh:load-docs into 640c44b on bigdatagenomics:master.

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@AmplabJenkins AmplabJenkins commented Jul 21, 2017

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2260/

Build result: FAILURE

[...truncated 15 lines...] > /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/1619/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 28082a5 # timeout=10Checking out Revision 28082a5 (origin/pr/1619/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 28082a5 > /home/jenkins/git2/bin/git rev-list 28082a5 # timeout=10Triggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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@fnothaft fnothaft left a comment

One small nit, otherwise LGTM!

@@ -2749,7 +2749,7 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
/**
* Load variants into a VariantRDD.
*
* If the path name has a .vcf/.vcf.gz/.vcf.bgzf/.vcf.bgz extension, load as VCF format.
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@fnothaft fnothaft Jul 21, 2017

Due to Hadoop codec limitations, we don't support .bgzf on load. We support it on write since we choose the output codec, but there's no .bgzf codec and the codecs are autodetected on read from the file extensions.

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@heuermh heuermh Jul 21, 2017

Yep, that is why I removed it. Only .bgz is supported on load, right?

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@fnothaft fnothaft Jul 21, 2017

Oh sorry about that, I misread the diff. .bgz and .gz are both supported.

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@heuermh heuermh commented Jul 21, 2017

Jenkins, retest this please.

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@coveralls coveralls commented Jul 21, 2017

Coverage Status

Coverage increased (+0.5%) to 84.743% when pulling 65a3c44 on heuermh:load-docs into 640c44b on bigdatagenomics:master.

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@coveralls coveralls commented Jul 21, 2017

Coverage Status

Coverage increased (+0.04%) to 84.287% when pulling 65a3c44 on heuermh:load-docs into 640c44b on bigdatagenomics:master.

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@AmplabJenkins AmplabJenkins commented Jul 21, 2017

Test PASSed.
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Test PASSed.

@fnothaft fnothaft merged commit 05b96be into bigdatagenomics:master Jul 21, 2017
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@fnothaft fnothaft commented Jul 21, 2017

Merged! Thanks @heuermh!

@heuermh heuermh deleted the load-docs branch Jul 21, 2017
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@heuermh heuermh commented Jul 21, 2017

Thank you!

@heuermh heuermh added this to the 0.23.0 milestone Dec 7, 2017
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4 participants