[ADAM-1182] isSorted=true should write SO:coordinate in SAM/BAM/CRAM header. #1183

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fnothaft commented Sep 26, 2016

Resolves #1182. Moved to use SAMTextHeaderCodec + SAMFileWriter.writeHeader to
write the header, vs. relying on SAMFileWriter's internal header writing code.

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Test FAILed.
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Build result: FAILURE

GitHub pull request #1183 of commit 6e048b2 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /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 --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true 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/1183/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 8dd475d07255dfb1e612df2a6d91a5159e1d0c0a # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1183/merge^{commit} # timeout=10Checking out Revision 8dd475d07255dfb1e612df2a6d91a5159e1d0c0a (origin/pr/1183/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 8dd475d07255dfb1e612df2a6d91a5159e1d0c0aFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
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Build result: FAILURE

GitHub pull request #1183 of commit 6e048b2 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /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 --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true 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/1183/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 8dd475d07255dfb1e612df2a6d91a5159e1d0c0a # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1183/merge^{commit} # timeout=10Checking out Revision 8dd475d07255dfb1e612df2a6d91a5159e1d0c0a (origin/pr/1183/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 8dd475d07255dfb1e612df2a6d91a5159e1d0c0aFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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@heuermh

LGTM, with minor fix

@@ -337,6 +337,7 @@ class AlignmentRecordRDDSuite extends ADAMFunSuite {
val reads = ardd.rdd
val actualSortedPath = tmpFile("sorted.sam")
+ println(actualSortedPath)

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heuermh Sep 26, 2016

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remove this

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remove this

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@fnothaft

fnothaft Sep 26, 2016

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Sorry, left that in when debugging. Fixed!

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fnothaft Sep 26, 2016

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Sorry, left that in when debugging. Fixed!

[ADAM-1182] isSorted=true should write SO:coordinate in SAM/BAM/CRAM …
…header.


Resolves #1182. Moved to use SAMTextHeaderCodec + SAMFileWriter.writeHeader to
write the header, vs. relying on SAMFileWriter's internal header writing code.
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Merged via commit 58549b2

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heuermh commented Sep 26, 2016

Merged via commit 58549b2

@heuermh heuermh closed this Sep 26, 2016

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