[ADAM-1057] Remove workaround for gzip/BGZF compressed VCF headers

[heuermh]

Fixes #1057

Requires HadoopGenomics/Hadoop-BAM#106 to be merged and deployed as version 7.5.1-SNAPSHOT. Will need to be updated to 7.6.0 when that release is made.

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GitHub pull request #1060 of commit b6e8d3c 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/1060/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 1b4111f # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1060/merge^{commit} # timeout=10Checking out Revision 1b4111f (origin/pr/1060/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 1b4111fec822b4840b82843a90e6915b0023b8c7First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

[heuermh]

Jenkins, test this please.

Issue HadoopGenomics/Hadoop-BAM#106 has been closed and a new snapshot should have been deployed.

[heuermh]

Jenkins, retest this please.

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[fnothaft]

This will go to 7.5.1 when that pushes to Maven Central, right?

[heuermh]

7.6.0 was just released and has made it to Maven Central, so I'll push & rebase with the new version shortly

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[fnothaft]

Small nit for readability: can you change this to either org.seqdoop.hadoop_bam.util._ or split it up across multiple lines? I think we typically go to importing the whole package at 4 imports.

[fnothaft]

LGTM, modulo one import nit. Let me know when you've updated it, and I can merge. I'm looking forward to having this in, @heuermh!

[fnothaft]

Hmm, I'm having bad times running this on the cluster on the 1KG .vcf.gz files. Unfortunately, I'm getting an uninformative error—the exception isn't serializable, which throws yet another exception—let me try to debug that and get a useful error.

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[heuermh]

Rebased!

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[jpdna]

+1 This works fine for me on a compressed vcf
I'll merge tomorrow unless someone suggests otherwise

[jpdna]

Merged 308cc58
Thanks for the PR @heuermh!