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[ADAM-674] Delete Bam2ADAM. #680

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merged 1 commit into from May 27, 2015

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fnothaft commented May 27, 2015

Resolves #674.

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ryan-williams commented May 27, 2015

lgtm!

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/706/

Build result: FAILURE

[...truncated 36 lines...]Triggering ADAM-prb ? 2.10,2.2.0,centosTriggering ADAM-prb ? 2.10,2.3.0,centosADAM-prb ? 2.11,1.0.4,centos completed with result SUCCESSADAM-prb ? 2.11,2.2.0,centos completed with result SUCCESSADAM-prb ? 2.10,1.0.4,centos completed with result FAILUREADAM-prb ? 2.11,2.3.0,centos completed with result SUCCESSADAM-prb ? 2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.10,2.3.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'ERROR: Failed to notify endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'java.lang.IndexOutOfBoundsException: Index: 0, Size: 0 at java.util.LinkedList.checkElementIndex(LinkedList.java:553) at java.util.LinkedList.set(LinkedList.java:488) at hudson.model.Run.getLog(Run.java:1953) at com.tikal.hudson.plugins.notification.Phase.getLog(Phase.java:141) at com.tikal.hudson.plugins.notification.Phase.buildJobState(Phase.java:79) at com.tikal.hudson.plugins.notification.Phase.handle(Phase.java:42) at com.tikal.hudson.plugins.notification.JobListener.onCompleted(JobListener.java:36) at hudson.model.listeners.RunListener.fireCompleted(RunListener.java:199) at hudson.model.Run.execute(Run.java:1786) at hudson.matrix.MatrixBuild.run(MatrixBuild.java:306) at hudson.model.ResourceController.execute(ResourceController.java:98) at hudson.model.Executor.run(Executor.java:374)Failed to notify endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8' - java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/706/

Build result: FAILURE

[...truncated 36 lines...]Triggering ADAM-prb ? 2.10,2.2.0,centosTriggering ADAM-prb ? 2.10,2.3.0,centosADAM-prb ? 2.11,1.0.4,centos completed with result SUCCESSADAM-prb ? 2.11,2.2.0,centos completed with result SUCCESSADAM-prb ? 2.10,1.0.4,centos completed with result FAILUREADAM-prb ? 2.11,2.3.0,centos completed with result SUCCESSADAM-prb ? 2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.10,2.3.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'ERROR: Failed to notify endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'java.lang.IndexOutOfBoundsException: Index: 0, Size: 0 at java.util.LinkedList.checkElementIndex(LinkedList.java:553) at java.util.LinkedList.set(LinkedList.java:488) at hudson.model.Run.getLog(Run.java:1953) at com.tikal.hudson.plugins.notification.Phase.getLog(Phase.java:141) at com.tikal.hudson.plugins.notification.Phase.buildJobState(Phase.java:79) at com.tikal.hudson.plugins.notification.Phase.handle(Phase.java:42) at com.tikal.hudson.plugins.notification.JobListener.onCompleted(JobListener.java:36) at hudson.model.listeners.RunListener.fireCompleted(RunListener.java:199) at hudson.model.Run.execute(Run.java:1786) at hudson.matrix.MatrixBuild.run(MatrixBuild.java:306) at hudson.model.ResourceController.execute(ResourceController.java:98) at hudson.model.Executor.run(Executor.java:374)Failed to notify endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8' - java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
Test FAILed.

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Just updated the jenkins-test script which relied on bam2adam (hence the test failure).

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fnothaft commented May 27, 2015

Just updated the jenkins-test script which relied on bam2adam (hence the test failure).

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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/707/
Test PASSed.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/707/
Test PASSed.

laserson added a commit that referenced this pull request May 27, 2015

@laserson laserson merged commit 2856c64 into bigdatagenomics:master May 27, 2015

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laserson May 27, 2015

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Merged. Thanks @fnothaft!

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laserson commented May 27, 2015

Merged. Thanks @fnothaft!

@fnothaft fnothaft deleted the fnothaft:remove-bam2adam branch May 27, 2015

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