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[ADAM-595] Delete the 'comparisons' code. #596

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tdanford commented Mar 1, 2015

This means deleting the comparisons code here; these files (Comparisons,
AvailableComparisons, and GeneratorFilter) are moving into the qc-metrics
package, along with the ComparisonsTraversalEngine.

Also being deleted are the test-suites for each of these classes.

Finally, the CLI commands which use these classes, CompareADAM and
FindReads, are also being deleted.

Each of these classes will be moved into the qc-metrics repository as
part of a separate pull request.

This resolves #595

[ADAM-595] Delete the 'comparisons' code.
This means deleting the comparisons code here; these files (Comparisons,
AvailableComparisons, and GeneratorFilter) are moving into the qc-metrics
package, along with the ComparisonsTraversalEngine.

Also being deleted are the test-suites for each of these classes.

Finally, the CLI commands which use these classes, CompareADAM and
FindReads, are also being deleted.

Each of these classes will be moved into the qc-metrics repository as
part of a separate pull request.
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Test PASSed.
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Test PASSed.
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Test PASSed.

[ADAM-595] Deleting the genotype- and variant- concordance classes.
ConcordanceTable and GenotypesSummary, as well as the concordance function from
VariationRDDFunctions (in GenotypeRDDFunctions) are all being deleted, along with
their tests.

Also going are the GenotypeConcordance and SummarizeGenotypes commands from the CLI.

All of this is being moved over to qc-metrics.
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Test PASSed.
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Test PASSed.
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Test PASSed.

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Test FAILed.
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Build result: FAILURE

GitHub pull request #596 of commit 4aa7af1 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[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/596/merge^{commit} # timeout=10Checking out Revision f260cb8edca472db9423a4964cc659f235caddd3 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f f260cb8edca472db9423a4964cc659f235caddd3 > git rev-list 329a72a # timeout=10Triggering 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 #596 of commit 4aa7af1 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[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/596/merge^{commit} # timeout=10Checking out Revision f260cb8edca472db9423a4964cc659f235caddd3 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f f260cb8edca472db9423a4964cc659f235caddd3 > git rev-list 329a72a # timeout=10Triggering 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.

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Jenkins, retest this please.

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fnothaft commented Mar 1, 2015

Jenkins, retest this please.

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If this builds, Frank, I think it's ready to go.

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tdanford commented Mar 1, 2015

If this builds, Frank, I think it's ready to go.

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fnothaft added a commit that referenced this pull request Mar 2, 2015

Merge pull request #596 from tdanford/moving-metrics
[ADAM-595] Delete the 'comparisons' code.

@fnothaft fnothaft merged commit eb67063 into bigdatagenomics:master Mar 2, 2015

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Let's cut it loose! Thanks @tdanford!

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fnothaft commented Mar 2, 2015

Let's cut it loose! Thanks @tdanford!

@tdanford tdanford deleted the tdanford:moving-metrics branch Mar 2, 2015

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Thanks @fnothaft.

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tdanford commented Mar 2, 2015

Thanks @fnothaft.

@danvk danvk referenced this pull request Jun 29, 2015

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Update to Adam 0.17 #310

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