Merge pull request #16 from dbmi-bgm/manta_cf_fix

SV confidence classes + Tests fixed
dbmi-bgm · Oct 21, 2022 · f732f7a · f732f7a
2 parents bfdd56a + 20fa372
commit f732f7a
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Showing 6 changed files with 11 additions and 28 deletions.
diff --git a/dockerfiles/sv_germline_granite/scripts/SV_confidence.py b/dockerfiles/sv_germline_granite/scripts/SV_confidence.py
@@ -132,37 +132,20 @@ def calculate_confidence_manta(vnt_obj):
         # currently we do not assign confidence to insertions
         if svtype == INSERTION_SVTYPE_MANTA:
             confidence = NA
-
-        elif (
-            (svlen > 250 or svtype == TRANSLOCATION_SVTYPE_MANTA)
-            and (
-                SR_alt >= 5
-                and PR_alt >= 5
-                and prop_spanning_reads >= 0.3
-                and prop_split_reads >= 0.3
-            )
-        ) or (
-            svlen <= 250
-            and svtype != TRANSLOCATION_SVTYPE_MANTA
-            and SR_alt > 5
-            and prop_split_reads > 0.3
+        elif (svlen > 250 or svtype == TRANSLOCATION_SVTYPE_MANTA) and (
+            SR_alt >= 5
+            and PR_alt >= 5
+            and prop_spanning_reads >= 0.3
+            and prop_split_reads >= 0.3
         ):
 
             confidence = HIGH_CONFIDENCE
 
-        elif (
-            (svlen > 250 or svtype == TRANSLOCATION_SVTYPE_MANTA)
-            and (
-                SR_alt >= 3
-                and PR_alt >= 3
-                and prop_spanning_reads >= 0.3
-                and prop_split_reads >= 0.3
-            )
-        ) or (
-            svlen <= 250
-            and svtype != TRANSLOCATION_SVTYPE_MANTA
-            and SR_alt > 3
-            and prop_split_reads > 0.3
+        elif (svlen > 250 or svtype == TRANSLOCATION_SVTYPE_MANTA) and (
+            SR_alt >= 3
+            and PR_alt >= 3
+            and prop_spanning_reads >= 0.3
+            and prop_split_reads >= 0.3
         ):
 
             confidence = MEDIUM_CONFIDENCE

diff --git a/...sv_germline_granite/scripts/test/files/confidence_classes_manta_3_genotype_ids_out.vcf.gz b/...sv_germline_granite/scripts/test/files/confidence_classes_manta_3_genotype_ids_out.vcf.gz
diff --git a/dockerfiles/sv_germline_granite/scripts/test/files/confidence_classes_manta_in.vcf.gz b/dockerfiles/sv_germline_granite/scripts/test/files/confidence_classes_manta_in.vcf.gz
diff --git a/dockerfiles/sv_germline_granite/scripts/test/files/confidence_classes_manta_out.vcf.gz b/dockerfiles/sv_germline_granite/scripts/test/files/confidence_classes_manta_out.vcf.gz
diff --git a/dockerfiles/sv_germline_granite/scripts/test/files/cytoband_test_fail2.vcf.gz b/dockerfiles/sv_germline_granite/scripts/test/files/cytoband_test_fail2.vcf.gz
diff --git a/dockerfiles/sv_germline_granite/scripts/test/test_SV_cytoband.py b/dockerfiles/sv_germline_granite/scripts/test/test_SV_cytoband.py
@@ -54,7 +54,7 @@ def test_end_not_found():
     #Variables
     args = {'inputvcf': 'test/files/cytoband_test_fail2.vcf.gz','outputfile':'output.vcf','cytoband':'test/files/cytoBand.txt'}
     # Run and Tests
-    with pytest.raises(Exception, match="Unexpected variant format found - END not in 0th position of INFO. Quitting"):
+    with pytest.raises(Exception, match="ERROR in variant INFO field, END tag is missing"):
         main_SV_cytoband(args)
 
 def test_multiple_start_cytobands():