Add loadReadsFromSamString function into ADAMContext

[xubo245]

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

[AmplabJenkins]

Can one of the admins verify this patch?

[fnothaft]

Jenkins, test this please.

[coveralls]

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

[AmplabJenkins]

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]

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

Where error in my code?

[fnothaft]

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]

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]

Jenkins, test this please.

[coveralls]

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

[AmplabJenkins]

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]

Jenkins, test this please.

[coveralls]

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

[AmplabJenkins]

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]

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

[xubo245]

Is it correct that the conflicts be resolved? @fnothaft

[xubo245]

Cloud it be merge?

It is second time that show conflicts with ADAMContext.scala

[heuermh]

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

[xubo245]

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

[xubo245]

This PR has more than a month...

[xubo245]

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

[heuermh]

@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]

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]

Closing in favor of sending users to the pipe API.

[xubo245]

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