Innocuous housekeeping changes in the partially determined haplotypes code #8361
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Github actions tests reported job failures from actions build 5250024693
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Github actions tests reported job failures from actions build 5250310142
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jamesemery
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Jun 16, 2023
| @@ -939,4 +939,9 @@ public AssemblyResultSet generateEmptyLLocalAssemblyResult(final AssemblyRegion | |||
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| return resultSet; | |||
| } | |||
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| private static String dotFileName(final Haplotype refHaplotype, final int kmerSize, final String suffix) { | |||
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this can probably know that the suffix is ".dot"... also there is some logic that could go into this for the ordering of the steps (0.4->1.0->1.4 etc...) i suppose its too much to ask that the order of steps be managed by some tool...
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I wrote said tool. Was it overkill?
.../hellbender/tools/walkers/haplotypecaller/PartiallyDeterminedHaplotypeComputationEngine.java
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Okay @jamesemery, ready for the next round of review. |
jamesemery
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Jun 23, 2023
| @@ -214,4 +215,42 @@ public void testDeletionUnderlapingDeterminedBases() { | |||
| Assert.assertEquals(result.getCigar(), TextCigarCodec.decode("10M")); | |||
| Assert.assertEquals(result.getDeterminedPosition(), DEL_AA_105.getStart()); | |||
| } | |||
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| @Test | |||
| public void testEventsOverlapForPDHapsCode() { | |||
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👍 i think we are going to appreciate having this unit test in some vague undetermined point in the future
...institute/hellbender/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java
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@jamesemery Getting into the
PartiallyDeterminedHaplotypeComputationEnginenow. No change in output here. I don't think there's anything controversial here. The commit history is discrete and pristine.My next DRAGEN PR might be where the fun begins.