Fixed Concordance tool to allow for no variation alleles in the truth data. #5718
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Codecov Report
@@ Coverage Diff @@
## master #5718 +/- ##
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- Coverage 87.069% 87.067% -0.003%
- Complexity 31875 31880 +5
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Files 1940 1940
Lines 146738 146756 +18
Branches 16226 16229 +3
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+ Hits 127764 127776 +12
- Misses 13061 13065 +4
- Partials 5913 5915 +2
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davidbenjamin
approved these changes
Feb 26, 2019
| // we assume that the truth has a single alternate allele | ||
| final boolean containsAltAllele = eval.getAlternateAlleles().contains(truth.getAlternateAllele(0)); | ||
| final boolean containsAltAllele = |
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You need to update the comment on line 294.
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| @Test | ||
| public void testDoesNotCrashWithNO_VARIATIONAlleles() { | ||
| final String testDir = toolsTestDir + "concordance/"; |
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This appears elsewhere in this test class, so perhaps extract a static constant for it.
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Sounds good! Fixed!
| runCommandLine(args); | ||
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| try { | ||
| final ConcordanceSummaryRecord.Reader reader = new ConcordanceSummaryRecord.Reader(summary); |
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There's some strange spacing here.
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Ah. I didn't reformat the code before I checked it in. I like to align my blocks of variable definitions.
Fixed!
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Fixed Concordance tool to allow for no variation alleles in the truth data.