Add quality score binner #1485
Merged
Add quality score binner #1485
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
Test FAILed. Build result: FAILURE[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1485/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains d0fb3edd7021762f878ef7a5ab66ab37dd25c38e # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1485/merge^{commit} # timeout=10Checking out Revision d0fb3edd7021762f878ef7a5ab66ab37dd25c38e (origin/pr/1485/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f d0fb3edd7021762f878ef7a5ab66ab37dd25c38eFirst 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 FAILUREADAM-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 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 SUCCESSNotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
|
Jenkins, retest this please. |
|
Test PASSed. |
heuermh
requested changes
Apr 12, 2017
| @@ -115,6 +115,8 @@ class TransformArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs { | |||
| var mdTagsFragmentSize: Long = 1000000L | |||
| @Args4jOption(required = false, name = "-md_tag_overwrite", usage = "When adding MD tags to reads, overwrite existing incorrect tags.") | |||
| var mdTagsOverwrite: Boolean = false | |||
| @Args4jOption(required = false, name = "-bin_quality_scores", usage = "Rewrites quality scores of reads into bins. User must provide bin description string.") | |||
There was a problem hiding this comment.
How about
Rewrites quality scores of reads into bins from a string of bin descriptions, e.g. 0,20,10;20,40,30.
| // if we have multiple bins, validate them | ||
| // - check that we don't have gaps between bins | ||
| // - check that we don't have overlapping bins | ||
| if (bins.size > 1) { |
There was a problem hiding this comment.
would this check be better in QualityScoreBin.apply?
|
I'd be ok merging this with the doc string fix suggested above |
Resolves bigdatagenomics#1462. Adds an API for binning quality scores to `AlignmentRecordRDD` and `FragmentRDD`. Exposes this on the `Transform` CLI.
fnothaft
force-pushed
the
issues/1462-quality-score-binner
branch
from
2d9cb2c
to
a089670
Compare
|
@heuermh addressed the doc issue. This is good to go from my side. |
|
Test PASSed. |
heuermh
approved these changes
May 12, 2017
|
Thank you, @fnothaft |
fnothaft
added a commit
to fnothaft/adam
that referenced
this pull request
May 21, 2017
…formFragments` Resolves bigdatagenomics#1359. Also, propegates the quality score binner (bigdatagenomics#1485) up to the `transformFragments` CLI.
fnothaft
added a commit
to fnothaft/adam
that referenced
this pull request
May 26, 2017
…formFragments` Resolves bigdatagenomics#1359. Also, propegates the quality score binner (bigdatagenomics#1485) up to the `transformFragments` CLI.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Resolves #1462. WIP. Still need to: