New, improved, rewritten assembler #127
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Test PASSed. |
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Hi Frank, Happy New Year! Thank you for the nice updates, though I seem to be getting some weird errors when I run Thanks, |
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@pgrosu thanks; happy new years to you too! As for the compile issue, it looks like you're building from an out-of-date repository. The |
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I think I did a little too much celebrating during the New Year, and only ran the clone without the pull. Running the following steps made it all better :) Thanks Frank! |
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Ah! No worries; glad to hear things are working now. |
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I added documentation, so this now depends on #129. |
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Test FAILed. Build result: FAILUREGitHub pull request #127 of commit f22c078 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-02 (centos) in workspace /home/jenkins/workspace/avocado-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/avocado.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/avocado.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/avocado.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/127/merge^{commit} # timeout=10Checking out Revision d16281d (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f d16281d > git rev-list 343b70d # timeout=10Triggering avocado-prb ? 1.0.4,centosTriggering avocado-prb ? 2.3.0,centosTriggering avocado-prb ? 2.2.0,centosavocado-prb ? 1.0.4,centos completed with result FAILUREavocado-prb ? 2.3.0,centos completed with result FAILUREavocado-prb ? 2.2.0,centos completed with result FAILURETest FAILed. |
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Test FAILed. Build result: FAILUREGitHub pull request #127 of commit 5b81229 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-02 (centos) in workspace /home/jenkins/workspace/avocado-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/avocado.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/avocado.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/avocado.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/127/merge^{commit} # timeout=10Checking out Revision d9a4a2d (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f d9a4a2d > git rev-list 343b70d # timeout=10Triggering avocado-prb ? 2.3.0,centosTriggering avocado-prb ? 1.0.4,centosTriggering avocado-prb ? 2.2.0,centosavocado-prb ? 2.3.0,centos completed with result FAILUREavocado-prb ? 1.0.4,centos completed with result FAILUREavocado-prb ? 2.2.0,centos completed with result FAILURETest FAILed. |
| </dependency> | ||
| <dependency> | ||
| <groupId>org.seqdoop</groupId> | ||
| <artifactId>cofoja</artifactId> |
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Is this a separate dist of the cofoja library than what we were depending on elsewhere? Did cofoja (do we know) ever get itself in working order for Java 1.8? That was an issue, a while ago...
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Nah, this is the same Cofoja. Cofoja is a won't fix for Java 8, IIRC, but was removed from the latest version of HTSJDK/Picard. Howaaaaver, no one has cut a new release of HTSJDK yet. See samtools/htsjdk#115 (comment).
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Jenkins, retest this please. |
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Test FAILed. Build result: FAILUREGitHub pull request #127 of commit 5b81229 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-02 (centos) in workspace /home/jenkins/workspace/avocado-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/avocado.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/avocado.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/avocado.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/127/merge^{commit} # timeout=10Checking out Revision d9a4a2d (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f d9a4a2d > git rev-list 63afcba # timeout=10Triggering avocado-prb ? 2.3.0,centosTriggering avocado-prb ? 1.0.4,centosTriggering avocado-prb ? 2.2.0,centosavocado-prb ? 2.3.0,centos completed with result FAILUREavocado-prb ? 1.0.4,centos completed with result FAILUREavocado-prb ? 2.2.0,centos completed with result FAILURETest FAILed. |
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Test PASSed. |
| val kmerSequences = KmerGraph.getKmerSequences(startFlank, kmerLength) ++ KmerGraph.getKmerSequences(endFlank, kmerLength) | ||
| addSequencesToGraph(kmerSequences, true) | ||
| override def toString(): String = { | ||
| "Sources: " + sourceKmers.map(_.kmerSeq).reduce(_ + ", " + _) + "\n" + |
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same mkString comment as above.
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Rebased on #131 and added an active region threshold. |
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Test PASSed. |
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Test FAILed. Build result: FAILUREGitHub pull request #127 of commit fea3a9c automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-02 (centos) in workspace /home/jenkins/workspace/avocado-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/avocado.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/avocado.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/avocado.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/127/merge^{commit} # timeout=10Checking out Revision a6dc5f0 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f a6dc5f0 > git rev-list 63afcba # timeout=10Triggering avocado-prb ? 1.0.4,centosTriggering avocado-prb ? 2.2.0,centosTriggering avocado-prb ? 2.3.0,centosavocado-prb ? 1.0.4,centos completed with result FAILUREavocado-prb ? 2.2.0,centos completed with result FAILUREavocado-prb ? 2.3.0,centos completed with result FAILURETest FAILed. |
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Test PASSed. |
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…ot have alt/ref observations.
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Test PASSed. |
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Test PASSed. |
This was referenced Apr 25, 2015
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Resolves #97. Eliminates most of the old assembler code. Adds a new assembler that emits observations directly from the de Brujin graph. In the old assembler, we generated haplotypes and realigned the reads to the haplotypes before calculating genotype likelihoods. In this assembler, we can handle longer haplotypes, and we eliminate the need to realign reads.