Merge pull request #3 from amplab/master

don't check allele match when evaluating SVs at exact breakpoint
amplab · May 19, 2014 · dc5ed97 · dc5ed97
2 parents a1e3bbe + b9f9078
commit dc5ed97
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Showing 3 changed files with 48 additions and 24 deletions.
diff --git a/smashbenchmarking/vcf_eval/eval_helper.py b/smashbenchmarking/vcf_eval/eval_helper.py
@@ -89,6 +89,8 @@ def get_var(variants):
         return variants.all_variants[loc]
     true_var = get_var(true_variants)
     pred_var = get_var(pred_variants)
+    if true_var.var_type.startswith("SV"):
+        return true_var.var_type == pred_var.var_type
     if ( true_var.var_type != pred_var.var_type ):
         return False
     return true_var.alt == pred_var.alt

diff --git a/test/chrom_stats.py b/test/chrom_stats.py
@@ -202,30 +202,6 @@ def test_false_neg_sv_ins(self):
         self.falseNegative(stat_reporter,VARIANT_TYPE.SV_INS)
         self.trueNegative(stat_reporter,VARIANT_TYPE.SV_DEL)
 
-    def test_bad_sv_ins(self):
-        pred_str = """##fileformat=VCFv4.0\n
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
-##source=TVsim\n
-#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
-chr19   88013   .       CTT     C       20      PASS    .       GT      0/1\n
-chr19   89272   .       C       T       20      PASS    .       GT      0/1\n
-chr19   269751  .       A       AAAAGAAAGGCATGACCTATCCTTTTATGCCACCTGGATGGACCTCACAGGCACACTGCTTCATGAGAGAG 20      PASS    .       GT      1/1
-"""
-
-        pred_io = StringIO.StringIO(pred_str)
-        pred_vcf = vcf.Reader(pred_io)
-        pred_vars = Variants(pred_vcf, MAX_INDEL_LEN)
-
-        sv_eps = 100
-
-        stat_reporter, errors = evaluate_variants(self.true_vars, pred_vars, sv_eps, sv_eps, None, None, None)
-
-        self.truePositive(stat_reporter,VARIANT_TYPE.SNP)
-        self.trueNegative(stat_reporter,VARIANT_TYPE.INDEL_INS)
-        self.truePositive(stat_reporter,VARIANT_TYPE.INDEL_DEL)
-        self.badCallAtTrueSite(stat_reporter,VARIANT_TYPE.SV_INS)
-        self.trueNegative(stat_reporter,VARIANT_TYPE.SV_DEL)
-
     def test_sv_snp_collision(self):
         pred_str = """##fileformat=VCFv4.0\n
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n

diff --git a/test/eval_helper.py b/test/eval_helper.py
@@ -124,6 +124,52 @@ def testChromEvaluateVariants(self):
         # TODO test known false positive functionality
         # TODO test genotype concordance
         pass
+    def testChromEvaluateVariantsSV(self):
+        #NB: SVs aren't rescued, just checked for within breakpoint tolerance
+        true_str = """##fileformat=VCFv4.0\n
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
+#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
+chr1   6   .       C     CGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGAAAAA       20      PASS    .       GT      0/1
+"""
+        #SV with exact position, exact allele match
+        pred_str = """##fileformat=VCFv4.0\n
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
+#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
+chr1   6   .       C     CGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGAAAAA       20      PASS    .       GT      0/1
+"""
+        true_vars = vcf_to_ChromVariants(true_str,'chr1')
+        pred_vars = vcf_to_ChromVariants(pred_str,'chr1')
+        cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
+        self.assertEqual(cvs.num_tp[VARIANT_TYPE.SV_INS],1)
+        #SV with exact position, difference allele match
+        pred_str = """##fileformat=VCFv4.0\n
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
+#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
+chr1   6   .       C     CGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGAAAAATGC       20      PASS    .       GT      0/1
+"""
+        pred_vars = vcf_to_ChromVariants(pred_str,'chr1')
+        cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
+        self.assertEqual(cvs.num_tp[VARIANT_TYPE.SV_INS],1)
+        #SV with position within tolerance, exact allele match
+        pred_str = """##fileformat=VCFv4.0\n
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
+#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
+chr1   4   .       C     CGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGAAAAA       20      PASS    .       GT      0/1
+"""
+
+        pred_vars = vcf_to_ChromVariants(pred_str,'chr1')
+        cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
+        self.assertEqual(cvs.num_tp[VARIANT_TYPE.SV_INS],1)
+        #SV outside of tolerance
+        pred_str = """##fileformat=VCFv4.0\n
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
+#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001\n
+chr1   110   .       C     CGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGAAAAA       20      PASS    .       GT      0/1
+"""
+        pred_vars = vcf_to_ChromVariants(pred_str,'chr1')
+        cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
+        self.assertEqual(cvs.num_tp[VARIANT_TYPE.SV_INS],0)
+
 
     def testRescueChromEvalVariants(self):
         pred_str = """##fileformat=VCFv4.0\n