v4.10.0 - Add additional properties to annotations#586
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… ID builder for variants. add variantID to additional properties output. add VCVs to RCV and SCV entries
javild
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May 11, 2022
| if (!hasSCVIds) { | ||
| properties.add(new Property(null, SCVIDS, String.join(",", scvAccessions))); | ||
| } | ||
| getTraitAssociation(variantAnnotation, vcvId).setAdditionalProperties(properties); |
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@julie-sullivan this line should not be needed
javild
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May 11, 2022
| private static final String PHASE_DATA_URL_SEPARATOR = "\\+"; | ||
| private static final String VARIANT_STRING_FORMAT = "\\+"; | ||
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| private Variant parseVariant(String variantString) { |
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is this method being used anywhere?
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nope. copy paste error! removed.
javild
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May 11, 2022
| } | ||
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| @Test | ||
| public void testKPVPMNVs() throws Exception { |
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Avoid using "KPVP" in names etc. it's a very internal GeL acronym :)
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merged into new v4.10.0 branch. |
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There are two changes in this PR.
ClinVar - add associated scvIds, vcvIds, rcvIds to additional properties
MNVs - other variants considered as part of phased MNV annotation