[ADAM-1683] Pull in Spark-BAM as a secondary loading path. #1686
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fnothaft
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Aug 26, 2017
adam-relocations/pom.xml
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| </transformers> | ||
| <relocations> | ||
| <relocation> | ||
| <pattern>org.seqdoop</pattern> |
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As a heads up to @ryan-williams, if I was to go this route, I would also want to relocate the org.hammerlab classes in org.hammerlab:spark-bam into org.bdgenomics so that we're not publishing a JAR with org.hammerlab classes that don't match what your published org.hammerlab:spark-bam artifact contains. However, I can't relocate the org.hammerlab classes without breaking my compile. I'm not sure why, but Scala companion objects (or possibly implicits?) seem to get broken by the relocation process.
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Test FAILed. Build result: FAILURE[...truncated 15 lines...] > /home/jenkins/git2/bin/git 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/1686/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 6dcb712 # timeout=10Checking out Revision 6dcb712 (origin/pr/1686/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 6dcb712abcf1ac551eccbc4a94528cd1bede99b0First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,2.1.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.1.0,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.1.0,centosADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.1.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.1.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.1.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.1.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
| val readerFn = if (sc.hadoopConfiguration.getBoolean(ADAMContext.USE_SPARK_BAM, false)) { | ||
| def sparkBamRead(path: String): RDD[SAMRecord] = { | ||
| if (path.endsWith(".bam")) { | ||
| sc.loadBam(HLPath(path)) |
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I probably didn't make this clear but sc.loadReads is the intended main entry-point to spark-bam, and will handle .sam, .bam, and .cram (the latter by delegating straight to hadoop-bam; for .sam, it's a new implementation that is probably equivalens to hadoop-bam's… i.e. it's not designed to be faster/better for any reason, like the .bam support is).
Using spark-bam just for .bams is also reasonable, this is just FTR
pom.xml
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| <exclusions> | ||
| <exclusion> | ||
| <groupId>org.hammerlab</groupId> | ||
| <artifactId>iterator_2.10</artifactId> |
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curious why this was needed, if you recall?
pom.xml
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| @@ -535,6 +548,11 @@ | |||
| </exclusions> | |||
| </dependency> | |||
| <dependency> | |||
| <groupId>org.hammerlab</groupId> | |||
| <artifactId>spark-bam_2.10</artifactId> | |||
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spark-bam_2.10, you say 🤔 😁
is this here in anticipation of a world where that exists? j/w / trying to follow
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Test FAILed. Build result: FAILURE[...truncated 15 lines...] > /home/jenkins/git2/bin/git 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/1686/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 462ec82 # timeout=10Checking out Revision 462ec82 (origin/pr/1686/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 462ec825227d43af99edb0c7d5a3edd13d91ed28First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.10,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.11,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.0,centosTriggering ADAM-prb ? 2.6.2,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.0,centosADAM-prb ? 2.6.2,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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Test FAILed. Build result: FAILURE[...truncated 15 lines...] > /home/jenkins/git2/bin/git 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/1686/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains faed42e # timeout=10Checking out Revision faed42e (origin/pr/1686/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f faed42e549fc7fb1d537c09e39bc45d00b29a0ebFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.10,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.11,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.0,centosTriggering ADAM-prb ? 2.6.2,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.0,centosADAM-prb ? 2.6.2,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.0,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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Test FAILed. Build result: FAILURE[...truncated 15 lines...] > /home/jenkins/git2/bin/git 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/1686/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains faed42e # timeout=10Checking out Revision faed42e (origin/pr/1686/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f faed42e549fc7fb1d537c09e39bc45d00b29a0ebFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.10,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.11,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.0,centosTriggering ADAM-prb ? 2.6.2,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.0,centosADAM-prb ? 2.6.2,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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Test FAILed. Build result: FAILURE[...truncated 15 lines...] > /home/jenkins/git2/bin/git 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/1686/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 084f071 # timeout=10Checking out Revision 084f071 (origin/pr/1686/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 084f0718d12a68fed77c2ae64c750eafbcc70d3eFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.11,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.10,1.6.3,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.11,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.0,centosTriggering ADAM-prb ? 2.6.2,2.10,1.6.3,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.0,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.0,centosADAM-prb ? 2.6.2,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,2.2.0,centos completed with result FAILUREADAM-prb ? 2.6.2,2.10,1.6.3,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.0,centos completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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Closing as WontFix. Feel free to create a new PR after rebasing against git head. |
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Resolves #1683. Not expected to compile for Spark 1.x/Scala 2.10.