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[ADAM-625] Enable globbing for BAM. #626

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merged 1 commit into from Mar 24, 2015

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fnothaft commented Mar 19, 2015

Resolves #625. Elaborates the glob before loading the header.

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GitHub pull request #626 of commit d48f1f1 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos) 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/626/merge^{commit} # timeout=10 > git branch -a --contains fd8f6a82ffc71c3b3d6b69977cb220f55a5e9b29 # timeout=10 > git rev-parse remotes/origin/pr/626/merge^{commit} # timeout=10Checking out Revision fd8f6a82ffc71c3b3d6b69977cb220f55a5e9b29 (origin/pr/626/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f fd8f6a82ffc71c3b3d6b69977cb220f55a5e9b29First time build. Skipping changelog.Triggering ADAM-prb ? 2.2.0,centosTriggering ADAM-prb ? 2.3.0,centosTriggering ADAM-prb ? 1.0.4,centosADAM-prb ? 2.2.0,centos completed with result FAILUREADAM-prb ? 2.3.0,centos completed with result FAILUREADAM-prb ? 1.0.4,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
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Build result: FAILURE

GitHub pull request #626 of commit d48f1f1 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos) 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/626/merge^{commit} # timeout=10 > git branch -a --contains fd8f6a82ffc71c3b3d6b69977cb220f55a5e9b29 # timeout=10 > git rev-parse remotes/origin/pr/626/merge^{commit} # timeout=10Checking out Revision fd8f6a82ffc71c3b3d6b69977cb220f55a5e9b29 (origin/pr/626/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f fd8f6a82ffc71c3b3d6b69977cb220f55a5e9b29First time build. Skipping changelog.Triggering ADAM-prb ? 2.2.0,centosTriggering ADAM-prb ? 2.3.0,centosTriggering ADAM-prb ? 1.0.4,centosADAM-prb ? 2.2.0,centos completed with result FAILUREADAM-prb ? 2.3.0,centos completed with result FAILUREADAM-prb ? 1.0.4,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Show outdated Hide outdated adam-cli/src/main/scala/org/bdgenomics/adam/cli/Transform.scala
@Args4jOption(required = false, name = "-force_load_fastq", usage = "Forces Transform to load from unpaired FASTQ.")
var forceLoadFastq: Boolean = false
@Args4jOption(required = false, name = "-force_load_fastq", usage = "Forces Transform to load from interleaved FASTQ.")
var forceLoadIFastq: Boolean = false

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laserson Mar 19, 2015

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did you mean fasta? or just one extra cmd+p?

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laserson Mar 19, 2015

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did you mean fasta? or just one extra cmd+p?

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fnothaft Mar 19, 2015

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There was a missing i --> interleaved; I had fixed it locally but forgot to commit before pushing.

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fnothaft Mar 19, 2015

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There was a missing i --> interleaved; I had fixed it locally but forgot to commit before pushing.

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lgtm after the build is fixed

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laserson commented Mar 19, 2015

lgtm after the build is fixed

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Test PASSed.
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massie Mar 24, 2015

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Thanks, Frank!

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massie commented Mar 24, 2015

Thanks, Frank!

massie added a commit that referenced this pull request Mar 24, 2015

Merge pull request #626 from fnothaft/glob-bams
[ADAM-625] Enable globbing for BAM.

@massie massie merged commit 40d1486 into bigdatagenomics:master Mar 24, 2015

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@fnothaft fnothaft deleted the fnothaft:glob-bams branch Mar 26, 2015

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