export valid fastq #856
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export valid fastq #856
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…ecord is null or "*". This gracefully fixes these records on import
…ecord is null or "*". This gracefully fixes these records on import
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Test FAILed. Build result: FAILUREGitHub pull request #856 of commit a380305 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/856/merge^{commit} # timeout=10 > git branch -a --contains c882546 # timeout=10 > git rev-parse remotes/origin/pr/856/merge^{commit} # timeout=10Checking out Revision c882546 (origin/pr/856/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f c8825467fdc55ad18cebac641804db2749da1011First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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@allenday Jenkins is reporting a test failure but only with Hadoop 2.6.0 and Spark 1.4.1 |
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Jenkins, retest this please. |
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Test FAILed. Build result: FAILUREGitHub pull request #856 of commit a380305 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) 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/856/merge^{commit} # timeout=10 > git branch -a --contains c882546 # timeout=10 > git rev-parse remotes/origin/pr/856/merge^{commit} # timeout=10Checking out Revision c882546 (origin/pr/856/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f c8825467fdc55ad18cebac641804db2749da1011First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.4.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.4.1,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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Yes, I see it. I'll investigate this coming week. Should be minor, all my Sent with MailTrack On Fri, Oct 9, 2015 at 3:45 AM, Frank Austin Nothaft <
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Test PASSed. |
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@fnothaft test passing now |
| else | ||
| adamRecord.getOrigQual | ||
| else if (adamRecord.getQual == null) | ||
| "B" * seqLength |
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The wikipedia link above is dead, and it reads to me like B as unknown quality score is not universal across FASTQ records produced by different versions of Illumina software. Should this be a parameter presented to the user?
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The adam2fastq exported in the case of a sam with "" (unknown read quality) just exports the "". This is invalid fastq.
This PR addresses the issue by assigning quality value of "B" for each base - this is conventionally used for reads of unknown quality.
Additionally, reads loaded in from fastq are also assigned "B"-string for malformed records containing "*" for read quality.