Add loadReadsFromSamString function into ADAMContext #1434

xubo245 · Mar 10, 2017

add loadReadsFromSamString function into ADAMContext,
add some annotation for loadReadsFromSamString

I have finished it in adam-0.19.0 and update for Adam-0.21.1-SNAPSHOT today.

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

AmplabJenkins · Mar 10, 2017

Can one of the admins verify this patch?

fnothaft · Mar 10, 2017

Jenkins, test this please.

coveralls · Mar 10, 2017

Coverage increased (+0.1%) to 76.501% when pulling 63b0a6e on xubo245:ADAM_SNAPSHOT into 07c1982 on bigdatagenomics:master.

AmplabJenkins · Mar 10, 2017

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1853/

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.

xubo245 · Mar 11, 2017

I can not understand the FAILed information...It is different from mine.

Where error in my code?

fnothaft · Mar 14, 2017

Hi @xubo245! Similar to my comment on your other PR, this is just our source formatting check failing; you can fix this by running ./scripts/format-source. Let me know if you have any problems running that. Thank you again for the contribution, and I hope to make a review pass tomorrow!

xubo245 · Mar 14, 2017

I just run ./scripts/format-source success and PR in this issue.

Is it OK?

If there are any problem, please tell me in two hour, after two hour, I need to other city and stay about two days. Thanks.

fnothaft · Mar 14, 2017

Jenkins, test this please.

coveralls · Mar 14, 2017

Coverage increased (+0.4%) to 76.793% when pulling 3c6a2a4 on xubo245:ADAM_SNAPSHOT into 07c1982 on bigdatagenomics:master.

AmplabJenkins · Mar 14, 2017

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1865/

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.

fnothaft · Mar 14, 2017

Jenkins, test this please.

coveralls · Mar 14, 2017

Coverage increased (+0.4%) to 76.793% when pulling 3c6a2a4 on xubo245:ADAM_SNAPSHOT into 07c1982 on bigdatagenomics:master.

AmplabJenkins · Mar 14, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1868/
Test PASSed.

xubo245 · Mar 17, 2017

The conflicts need be resolved by me？ The conflicts should be change after I download the latest version

xubo245 · Mar 17, 2017

Is it correct that the conflicts be resolved? @fnothaft

xubo245 · Mar 27, 2017

Cloud it be merge?

It is second time that show conflicts with ADAMContext.scala

heuermh · Mar 27, 2017

@xubo245 sorry about the conflicts, we'll review and help rebase/squash commits after the 0.22.0 release is cut tomorrow.

xubo245 · Apr 9, 2017

@heuermh Clould you help me to deal with this commits ?

xubo245 · Apr 14, 2017

This PR has more than a month...

xubo245 · Apr 15, 2017

Cloud you help me to deal with this commits ? @fnothaft @heuermh

heuermh · Apr 17, 2017

@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?

xubo245 · Apr 17, 2017

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...
It has been described in #1425

I do not known what is the Pipe API .

fnothaft · Jan 9, 2018

Closing in favor of sending users to the pipe API.

xubo245 · Jan 10, 2018

@fnothaft You require me raise this PR before, but now don't merge...

xubo245 referenced this pull request Mar 10, 2017
Closed
Question:How to tranform a line of sam to AlignmentRecord? #1425

./scripts/format-source

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3c6a2a4

xubo245 referenced this pull request Mar 14, 2017
Closed
Add test sample(verify number of reads in loadAlignments function) and ADAM SNAPSHOT document #1433

Merge branch 'master' into ADAM_SNAPSHOT

4110702

xubo245 added some commits Mar 18, 2017

improve pull request quality

efadff4

improve pull request quality again

cd5f6ff

improve pull request quality: change Field name

3a6b0bb

improve pull request quality: change Field name again

e29c560

fnothaft added this to the 0.23.0 milestone Mar 22, 2017

Merge branch 'master' into ADAM_SNAPSHOT

72e1687

fnothaft modified the milestones: 0.24.0, 0.23.0 May 11, 2017

heuermh added this to Triage in Release 0.24.0 Jan 4, 2018

fnothaft closed this Jan 9, 2018

heuermh moved this from Triage to Completed in Release 0.24.0 Jan 9, 2018

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Add loadReadsFromSamString function into ADAMContext #1434

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xubo245 commented Mar 10, 2017 • edited

xubo245 added some commits Mar 10, 2017

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xubo245 referenced this pull request Mar 10, 2017

Question:How to tranform a line of sam to AlignmentRecord? #1425

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Build result: FAILURE

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xubo245 commented Mar 14, 2017 • edited

xubo245 referenced this pull request Mar 14, 2017

Add test sample(verify number of reads in loadAlignments function) and ADAM SNAPSHOT document #1433

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Build result: FAILURE

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xubo245 commented Apr 17, 2017 • edited

fnothaft modified the milestones: 0.24.0, 0.23.0 May 11, 2017

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xubo245 commented Mar 10, 2017 •

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