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[ADAM-1877] Add filterToReferenceName(s) to SequenceDictionary. #1995

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merged 3 commits into from Jul 4, 2018

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heuermh commented Jun 13, 2018

Fixes #1877. Work in progress.

@heuermh heuermh referenced this pull request Jun 13, 2018

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Add convenience method to filter by contig #1877

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coveralls commented Jun 13, 2018

Coverage Status

Coverage increased (+0.007%) to 79.493% when pulling eb30dba on heuermh:filter-by-contig into e7cbfcd on bigdatagenomics:master.

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AmplabJenkins commented Jun 13, 2018

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2770/
Test PASSed.

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LGTM. While you're at it though, I'd love a def filterByReferenceName(fn: (String) => Boolean): SequenceDictionary ;)

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AmplabJenkins commented Jun 28, 2018

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/1995/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains af23a96 # timeout=10Checking out Revision af23a96 (origin/pr/1995/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f af23a96d3bc418505f169fddc4565e1ea7cd325cFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,2.2.1,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.

@heuermh heuermh force-pushed the heuermh:filter-by-contig branch from 647529e to eb30dba Jun 28, 2018

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AmplabJenkins commented Jun 28, 2018

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2778/
Test PASSed.

@fnothaft fnothaft merged commit 46e466d into bigdatagenomics:master Jul 4, 2018

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Codacy/PR Quality Review Up to standards. A positive pull request.
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fnothaft commented Jul 4, 2018

Merged! Thanks @heuermh!

@heuermh heuermh deleted the heuermh:filter-by-contig branch Jul 4, 2018

@heuermh heuermh added this to the 0.24.1 milestone Jul 4, 2018

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