Fixed bug in VCF SV Filter wrapper and expanded coverage (#260)

snappy_wrappers/wrappers/vcf_sv_filter/vcf_sv_filter.py

@@ -405,7 +405,7 @@ def get_inner_region(self, record):
         else:
             # confidence intervals don't overlap
             pos_begin += ci_pos[1]
-            pos_end += ci_pos[0]  # negative
+            pos_end += ci_end[0]  # negative
             return GenomeRegion(record.CHROM, pos_begin, pos_end)
 
 

tests/snappy_wrappers/wrappers/test_vcf_sv_filter.py

@@ -0,0 +1,119 @@
+# -*- coding: utf-8 -*-
+"""Code for testing vcf_sv_filter wrapper"""
+
+import vcfpy
+
+from snappy_wrappers.wrappers.vcf_sv_filter.vcf_sv_filter import (
+    GenomeRegion,
+    MantaGenotypeMetricsBuilder,
+)
+
+
+def test_manta_genotype_metrics_builder_get_length_dup_no_end():
+    """Tests MantaGenotypeMetricsBuilder.get_length() - DUP no END"""
+    record = vcfpy.Record(
+        CHROM="chr1",
+        POS=500,
+        ID=[],
+        REF="A",
+        ALT=[vcfpy.SymbolicAllele("DUP")],
+        QUAL=None,
+        FILTER=[],
+        INFO=vcfpy.OrderedDict({"SVTYPE": "DUP"}),
+    )
+    actual = MantaGenotypeMetricsBuilder().get_length(record)
+    assert actual is None
+
+
+def test_manta_genotype_metrics_builder_get_length_del():
+    """Tests MantaGenotypeMetricsBuilder.get_length() - DEL"""
+    record = vcfpy.Record(
+        CHROM="chr1",
+        POS=500,
+        ID=[],
+        REF="A",
+        ALT=[vcfpy.SymbolicAllele("DEL")],
+        QUAL=None,
+        FILTER=[],
+        INFO=vcfpy.OrderedDict({"END": 1535, "SVTYPE": "DEL"}),
+    )
+    expected = 1036
+    actual = MantaGenotypeMetricsBuilder().get_length(record)
+    assert actual == expected
+
+
+def test_manta_genotype_metrics_builder_get_length_ins():
+    """Tests MantaGenotypeMetricsBuilder.get_length() - INS without SVLEN"""
+    record = vcfpy.Record(
+        CHROM="chr1",
+        POS=500,
+        ID=[],
+        REF="A",
+        ALT=[vcfpy.SymbolicAllele("INS")],
+        QUAL=None,
+        FILTER=[],
+        INFO=vcfpy.OrderedDict({"SVTYPE": "INS", "SVLEN": [1500, 9999]}),
+    )
+    expected = 1500  # first coordinate in list
+    actual = MantaGenotypeMetricsBuilder().get_length(record)
+    assert actual == expected
+
+
+def test_manta_genotype_metrics_builder_get_length_ins_no_svlen():
+    """Tests MantaGenotypeMetricsBuilder.get_length() - INS without SVLEN"""
+    record = vcfpy.Record(
+        CHROM="chr1",
+        POS=500,
+        ID=[],
+        REF="A",
+        ALT=[vcfpy.SymbolicAllele("INS")],
+        QUAL=None,
+        FILTER=[],
+        INFO=vcfpy.OrderedDict({"SVTYPE": "INS"}),
+    )
+    expected = 0  # default value
+    actual = MantaGenotypeMetricsBuilder().get_length(record)
+    assert actual == expected
+
+
+def test_manta_genotype_metrics_builder_get_inner_region():
+    """Tests MantaGenotypeMetricsBuilder.get_inner_region()"""
+    record = vcfpy.Record(
+        CHROM="chr1",
+        POS=500,
+        ID=[],
+        REF="A",
+        ALT=[vcfpy.SymbolicAllele("DEL")],
+        QUAL=None,
+        FILTER=[],
+        INFO=vcfpy.OrderedDict(
+            {
+                "END": 1535,
+                "SVTYPE": "DEL",
+                "SVLEN": [-1036],
+                "IMPRECISE": True,
+                "CIPOS": [-538, 538],
+                "CIEND": [-294, 294],
+                "SIZE_CLASS": "MEDIUM",
+            }
+        ),
+    )
+    expected = GenomeRegion("chr1", 1037, 1241)
+    actual = MantaGenotypeMetricsBuilder().get_inner_region(record)
+    assert actual == expected
+
+
+def test_manta_genotype_metrics_builder_get_inner_region_no_length():
+    """Tests MantaGenotypeMetricsBuilder.get_inner_region() - Length is None"""
+    record = vcfpy.Record(
+        CHROM="chr1",
+        POS=500,
+        ID=[],
+        REF="A",
+        ALT=[vcfpy.SymbolicAllele("DEL")],
+        QUAL=None,
+        FILTER=[],
+        INFO=vcfpy.OrderedDict({"SVTYPE": "DEL"}),
+    )
+    actual = MantaGenotypeMetricsBuilder().get_inner_region(record)
+    assert actual is None