[ADAM-822][ADAM-823] SAM follows @SQ order #824
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Test FAILed. Build result: FAILUREGitHub pull request #824 of commit 9ed8c99 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 > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/824/merge^{commit} # timeout=10 > git branch -a --contains e05ee91 # timeout=10 > git rev-parse remotes/origin/pr/824/merge^{commit} # timeout=10Checking out Revision e05ee91 (origin/pr/824/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f e05ee916e06d5d9abf59ad5110b077705f6b1b18First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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I am -0 on this change, because it breaks #784 and is only a partial fix for #823. I think this change can be rewritten to still support #784. Right now, we can't completely fix #823, which is why #784 is necessary. Specifically, this change only fixes #823 if you have the original |
| @@ -109,8 +109,7 @@ class SequenceDictionary(val records: Vector[SequenceRecord]) extends Serializab | |||
| * @return Returns a SAM formatted sequence dictionary. | |||
| */ | |||
| def toSAMSequenceDictionary: SAMSequenceDictionary = { | |||
| import SequenceRecord._ | |||
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There should be a parameter to choose if you wanted this sorted or not.
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Superceded by 283ea9d. |
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Not sure this works yet. Just ran into HadoopGenomics/Hadoop-BAM#21. Going to sleep now.