Add loadReadsFromSamString function into ADAMContext #1434
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Can one of the admins verify this patch? |
Jenkins, test this please. |
Test FAILed. Build result: FAILURE[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1434/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 86777ab # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1434/merge^{commit} # timeout=10Checking out Revision 86777ab (origin/pr/1434/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 86777abd59cd3f38efc86bb19fd76eb11707852cFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
I can not understand the FAILed information...It is different from mine. Where error in my code? |
Hi @xubo245! Similar to my comment on your other PR, this is just our source formatting check failing; you can fix this by running |
Jenkins, test this please. |
Test FAILed. Build result: FAILURE[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1434/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 57029b1 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1434/merge^{commit} # timeout=10Checking out Revision 57029b1 (origin/pr/1434/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 57029b136cfac82a7c1ad5f457a9f33b06e88c09First time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
Jenkins, test this please. |
Test PASSed. |
The conflicts need be resolved by me? The conflicts should be change after I download the latest version |
Is it correct that the conflicts be resolved? @fnothaft |
Cloud it be merge? It is second time that show conflicts with ADAMContext.scala |
@xubo245 sorry about the conflicts, we'll review and help rebase/squash commits after the 0.22.0 release is cut tomorrow. |
@heuermh Clould you help me to deal with this commits ? |
This PR has more than a month... |
@xubo245 I took a closer look at this last week. Even with the commits straightened out, I feel like I'm missing the use case. What would this provide that say the Pipe API does not? |
the use case: When we invoke read mapping tools in spark, read mapping return RDD(sam format), It need to transform Adam. If write to local Filesystem, it waste time... I do not known what is the Pipe API . |
Closing in favor of sending users to the pipe API. |
@fnothaft You require me raise this PR before, but now don't merge... |
add loadReadsFromSamString function into ADAMContext,
add some annotation for loadReadsFromSamString
link: #1425
I have finished it in adam-0.19.0 and update for Adam-0.21.1-SNAPSHOT today.
@fnothaft @heuermh
The first and second commits is not related about link: #1425. But I do not known how to remove it, sorry.
The two commits has been PR: #1433