Fixing bug when removing annotations from empty map #8870
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clean up better
ldgauthier
approved these changes
Jun 13, 2024
| @@ -701,4 +699,19 @@ public void testSpanDelRegression() throws IOException { | |||
| //no more star alleles because deletions are all gone | |||
| Assert.assertFalse(variants.stream().anyMatch(v -> v.getAlternateAlleles().contains(Allele.SPAN_DEL))); | |||
| } | |||
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| @Test | |||
| public void warnWhenRemovingAnnotations() { | |||
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I would change this name since this doesn't actually warn. Maybe "testRemoveAbsentAnnotation"?
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In an effort to make the Reblocking pipeline more user friendly we'd like to always have the option to remove the PRI annotation (which is incorrectly added by certain versions of dragen) from the GVCF turned on, even when PRI is not present in the input. There was an edge case that threw an exception when there were no FORMAT annotations, so this PR fixes that issue.