[ADAM-1497] Add union to GenomicRDD. #1526
Merged
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/1526/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains ce29373ec3eff23b4c14bc2a99f1a7a7a3efc59c # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1526/merge^{commit} # timeout=10Checking out Revision ce29373ec3eff23b4c14bc2a99f1a7a7a3efc59c (origin/pr/1526/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f ce29373ec3eff23b4c14bc2a99f1a7a7a3efc59cFirst 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. |
Resolves bigdatagenomics#1497. Also adds `size` methods to `SequenceDictionary` and `RecordGroupDictionary`. Requires the addition of a `ClassTag` to the `GenericGenomicRDD` case class.
fnothaft
force-pushed
the
issues/1497-union
branch
from
55cb7f9
to
7013184
Compare
|
Test PASSed. |
heuermh
requested changes
May 15, 2017
| val union = features1.union(features2) | ||
| assert(union.rdd.count === (features1.rdd.count + features2.rdd.count)) | ||
| // only a single contig between the two | ||
| assert(union.sequences.size === 1) |
There was a problem hiding this comment.
implies there is a distinct here . . .
There was a problem hiding this comment.
There is a filter by contig name when merging two SequenceDictionarys.
| val genotype2 = sc.loadGenotypes(testFile("small.vcf")) | ||
| val union = genotype1.union(genotype2) | ||
| assert(union.rdd.count === (genotype1.rdd.count + genotype2.rdd.count)) | ||
| assert(union.sequences.size === (genotype1.sequences.size + genotype2.sequences.size)) |
There was a problem hiding this comment.
... but not here. Does (_ ++ _) collapse elements that are equals?
There was a problem hiding this comment.
This case is everyone's jolly favorite bioinformatics boondoggle: chr prefixes vs no prefixes. Thus, the contigs are distinct.
There was a problem hiding this comment.
I know, I know. However, works for our test purposes.
|
Thank you, @fnothaft |
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 #1497. Also adds
sizemethods toSequenceDictionaryandRecordGroupDictionary. Requires the addition of aClassTagto theGenericGenomicRDDcase class.