CLI & mappability filter for region join, custom exceptions #421
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Test FAILed. Build result: FAILUREGitHub pull request #421 of commit 2e4c9c3 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/421/merge^{commit} # timeout=10Checking out Revision 8cd1077 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 8cd1077 > git rev-list db0f900 # 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 FAILURETest FAILed. |
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Test PASSed. |
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| //val uncounted: RDD[Feature] = features.subtract(counted.map(_._1)) | ||
| //counted.union(uncounted.map(f => (f, 0))) |
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Can you eliminate this dead code?
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@tdanford looks good! Can you rebase on master? |
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Test FAILed. Build result: FAILUREGitHub pull request #421 of commit 37bae7b 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/421/merge^{commit} # timeout=10Checking out Revision 02f3b8a (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 02f3b8a > git rev-list 77ea367 # timeout=10Triggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.3.0,centosADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.3.0,centos completed with result FAILURETest FAILed. |
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Just pinging for a rebase. |
Including UnmappedException as the first (typed) custom exception. This is so we can include/report better error messages from within ADAM processes.
There are two changes here: 1. RegionJoin.partitionAndJoin now pre-filters all records on either side of the join with a check that the records are mappable, and doesn't try to join those that aren't. 2. RegionJoin attempts to catch the NPE that comes from having non-mappable records sneak through, and throws an UnmappedException instead.
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Test FAILed. Build result: FAILUREGitHub pull request #421 of commit 3d212cd 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/421/merge^{commit} # timeout=10Checking out Revision d97959410432b7d8be1fcf05a37f34154857ed52 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f d97959410432b7d8be1fcf05a37f34154857ed52 > 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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Test FAILed. Build result: FAILUREGitHub pull request #421 of commit 27d515e 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/421/merge^{commit} # timeout=10Checking out Revision 4fb0507ce55f8a2b6bd334db1f3a185ba372705b (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 4fb0507ce55f8a2b6bd334db1f3a185ba372705b > 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. |
(don't know how/why this was dropped)
Also, fixed some imports in the CountReads class.
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Test PASSed. |
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@tdanford what's the status on this? Close and reopen later? |
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Closing due to inactivity. |
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Fixes #420, #297
Several changes:
partitionAndJoinmethod, fixing (I hope) Christos's problemhasReferenceRegiontoReferenceMapping-- to explicitly check for whether a value can be converted to a ReferenceRegion