Support unmapped reads in Spark. #3369
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lbergelson
previously requested changes
Aug 2, 2017
| return true; | ||
| } | ||
| if (traversalParameters.traverseUnmappedReads() && record.getReadUnmappedFlag() && record.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START) { |
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Could you add a comment for future generations explaining this case.
| { unmappedBam, null, Arrays.asList(publicTestDir + "org/broadinstitute/hellbender/engine/reads_data_source_test1_unmapped2.intervals"), Arrays.asList("a", "b", "c", "k", "u1", "u2", "u3", "u4", "u5") }, | ||
| { ceuSnippet, null, Arrays.asList("unmapped"), Arrays.asList("g", "h", "h", "i", "i") }, | ||
| { ceuSnippet, null, Arrays.asList("20:10000009-10000011", "unmapped"), Arrays.asList("a", "b", "c", "d", "e", "g", "h", "h", "i", "i") }, | ||
| { ceuSnippet, null, Arrays.asList("20:10000009-10000013", "unmapped"), Arrays.asList("a", "b", "c", "d", "e", "f", "f", "g", "h", "h", "i", "i") }, |
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We should add a test case here that is just an interval and not including unmapped, I'm sure it's covered by existing tests, but it would be good to have one here for completeness.
| } | ||
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| @Test(dataProvider = "UnmappedReadInclusionTestData") | ||
| public void testUnmappedReadInclusion( final File input, final String reference, final List<String> intervalStrings, final List<String> expectedReadNames ) { |
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We might want to make a matching test in ReadSparkSourceUnitTest that directly exercises getParallelReads.
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Thanks for the review @lbergelson. I've addressed all your comments. (Note the tests will still fail until there's a new Hadoop-BAM release.) |
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@lbergelson, @droazen are you OK with adding a SNAPSHOT dependency for Hadoop-BAM so we can commit this (and also the GVCF PR)? |
Codecov Report
@@ Coverage Diff @@
## master #3369 +/- ##
==============================================
+ Coverage 79.923% 79.94% +0.017%
- Complexity 17884 17897 +13
==============================================
Files 1198 1198
Lines 64966 64980 +14
Branches 10114 10120 +6
==============================================
+ Hits 51923 51945 +22
+ Misses 9010 9002 -8
Partials 4033 4033
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Not ready for merge as this relies on HadoopGenomics/Hadoop-BAM#136, hence a new Hadoop-BAM release.
Addresses #2572 and #2571