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Allow for export of query name sorted SAM files #2026

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merged 1 commit into from Oct 17, 2018

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karenfeng commented Aug 10, 2018

Creates function to sort reads by query name, and allows SAM files to be written with all sort orders.

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coveralls commented Aug 10, 2018

Coverage Status

Coverage decreased (-0.03%) to 78.906% when pulling 6ca7588 on karenfeng:exportQuerynameSortedBams into 8f4b4a4 on bigdatagenomics:master.

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AmplabJenkins commented Aug 10, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2794/

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/2026/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 339aa1b # timeout=10Checking out Revision 339aa1b (origin/pr/2026/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 339aa1b2b567c201fce05be2508eb3437b601dd6First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.2,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.2,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.2,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.2,centosADAM-prb ? 2.6.2,2.10,2.2.2,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.2,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.2,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.10,2.2.2,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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fnothaft commented Aug 11, 2018

Jenkins, retest this please.

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AmplabJenkins commented Aug 11, 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/2795/
Test PASSed.

@heuermh heuermh merged commit 2b40f25 into bigdatagenomics:master Oct 17, 2018

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heuermh commented Oct 17, 2018

Thank you, @karenfeng!

@heuermh heuermh added this to the 0.24.1 milestone Oct 17, 2018

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