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[ADAM-499] Add -onlyvariants option to vcf2adam #501

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laserson commented Nov 21, 2014

This will allow ingesting a variant-only VCF file (like the released ExAC data) to write Variant objects instead of Genotype objects.

Fixes #499.

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Nice! Great idea; this should also help a lot with broadcast object size for indel realignment and BQSR.

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fnothaft commented Nov 21, 2014

Nice! Great idea; this should also help a lot with broadcast object size for indel realignment and BQSR.

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Can you rebase this @laserson?

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fnothaft commented Nov 22, 2014

Can you rebase this @laserson?

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done.

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laserson commented Nov 22, 2014

done.

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Build result: FAILURE

GitHub pull request #501 of commit 73d097b automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (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/501/merge^{commit} # timeout=10Checking out Revision 362e45c (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 362e45c > git rev-list a111506 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILURE
Test FAILed.

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Build result: FAILURE

GitHub pull request #501 of commit 73d097b automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (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/501/merge^{commit} # timeout=10Checking out Revision 362e45c (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 362e45c > git rev-list a111506 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILURE
Test FAILed.

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scripts/format-source :)

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laserson commented Nov 22, 2014

scripts/format-source :)

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@laserson I lol'd when I saw it.

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fnothaft commented Nov 22, 2014

@laserson I lol'd when I saw it.

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fixed, but can i make it fail my local build?

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laserson commented Nov 22, 2014

fixed, but can i make it fail my local build?

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If you run scripts/jenkins-test, it should fail.

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fnothaft commented Nov 22, 2014

If you run scripts/jenkins-test, it should fail.

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I was racing to fix it before you commented again :)

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laserson commented Nov 22, 2014

I was racing to fix it before you commented again :)

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OK, now let's rebase this on #507.

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fnothaft commented Nov 22, 2014

OK, now let's rebase this on #507.

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Out of curiosity, I imagine this will simply merge cleanly as is. Do you want to rebase for aesthetic reasons? I.e., to get a linear chain of issue commit-merge commit "bubbles"?

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laserson commented Nov 22, 2014

Out of curiosity, I imagine this will simply merge cleanly as is. Do you want to rebase for aesthetic reasons? I.e., to get a linear chain of issue commit-merge commit "bubbles"?

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Do you want to rebase for aesthetic reasons? I.e., to get a linear chain of issue commit-merge commit "bubbles"?

Yep; that's the exact reason, actually.

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fnothaft commented Nov 22, 2014

Do you want to rebase for aesthetic reasons? I.e., to get a linear chain of issue commit-merge commit "bubbles"?

Yep; that's the exact reason, actually.

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Also, it appears that every time I rebase the code changes in a way that requires me to run format-source.

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laserson commented Nov 22, 2014

Also, it appears that every time I rebase the code changes in a way that requires me to run format-source.

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That's odd... Especially since the #507 change made no changes to code...? How many files needed to be reformatted?

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fnothaft commented Nov 22, 2014

That's odd... Especially since the #507 change made no changes to code...? How many files needed to be reformatted?

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fnothaft added a commit that referenced this pull request Nov 22, 2014

Merge pull request #501 from laserson/ADAM-499
[ADAM-499] Add -onlyvariants option to vcf2adam

@fnothaft fnothaft merged commit c4b4c50 into bigdatagenomics:master Nov 22, 2014

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Merged! Thanks @laserson!

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fnothaft commented Nov 22, 2014

Merged! Thanks @laserson!

@laserson laserson deleted the laserson:ADAM-499 branch Dec 2, 2014

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