Merge pull request #451 from ga4gh/issue-426

add RLE examples with SPDI annotations
ga4gh · Dec 16, 2023 · ae5cc61 · ae5cc61
2 parents 1b68dfb + 51ab262
commit ae5cc61
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diff --git a/examples/SPDI_contraction.yaml b/examples/SPDI_contraction.yaml
@@ -0,0 +1,16 @@
+type: Allele
+expressions:
+  - syntax: spdi
+    value: NC_000001.11:40819438:CTCCTCCT:CTCCT
+location:
+  type: SequenceLocation
+  sequenceReference:
+    refgetAccession: SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO
+    residueAlphabet: na
+    id: NC_000001.11
+  start: 40819438
+  end: 40819446
+state:
+  type: ReferenceLengthExpression
+  length: 5
+  repeatSubunitLength: 3
diff --git a/examples/SPDI_expansion.yaml b/examples/SPDI_expansion.yaml
@@ -0,0 +1,16 @@
+type: Allele
+expressions:
+  - syntax: spdi
+    value: NC_000001.11:40819438:CTCCTCCT:CTCCTCCTCCT
+location:
+  type: SequenceLocation
+  sequenceReference:
+    refgetAccession: SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO
+    residueAlphabet: na
+    id: NC_000001.11
+  start: 40819438
+  end: 40819446
+state:
+  type: ReferenceLengthExpression
+  length: 11
+  repeatSubunitLength: 3
diff --git a/tests/test_definitions.yaml b/tests/test_definitions.yaml
@@ -31,3 +31,11 @@ tests:
     description: A haplotype of two alleles on a shared chromosome reference sequence.
     schema: vrs
     definition: Haplotype
+  - test_file: SPDI_contraction.yaml
+    description: A simple RLE contraction from SPDI representation
+    schema: vrs
+    definition: Allele
+  - test_file: SPDI_expansion.yaml
+    description: A simple RLE expansion from SPDI representation
+    schema: vrs
+    definition: Allele