test v0.3.1

pirl-unc · Aug 6, 2024 · 0402dce · 0402dce
1 parent 932c4c9
commit 0402dce
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Showing 2 changed files with 8 additions and 1 deletion.
diff --git a/python/vstolib/vcf/clairs.py b/python/vstolib/vcf/clairs.py
@@ -151,6 +151,7 @@ def parse_clairs_callset(
         # Update the following variables if they are currently unknown but can be inferred:
         # total_read_count
         # alternate_allele_fraction
+        # reference_allele_read_count
         if alternate_allele_read_count >= 0 and \
             reference_allele_read_count >= 0 and \
             total_read_count == -1:
@@ -159,6 +160,10 @@ def parse_clairs_callset(
             total_read_count > 0 and \
             alternate_allele_fraction == -1.0:
             alternate_allele_fraction = float(alternate_allele_read_count) / float(total_read_count)
+        if alternate_allele_read_count >= 0 and \
+            total_read_count > 0 and \
+            reference_allele_read_count <= 0:
+            reference_allele_read_count = total_read_count - alternate_allele_read_count
 
         # Append variant call to variants list
         variant_call_id = '%s_%s_%s_%i_%s_%s:%i_%s:%i' % (

diff --git a/python/vstolib/vcf/common.py b/python/vstolib/vcf/common.py
@@ -80,7 +80,9 @@ def get_attribute_types(variant_calling_method: str) -> Dict:
     """
     Get the attribute type dictionary for a variant calling method.
     """
-    if variant_calling_method == VariantCallingMethods.CUTESV:
+    if variant_calling_method == VariantCallingMethods.CLAIRS:
+        return VariantCallingMethods.AttributeTypes.CLAIRS
+    elif variant_calling_method == VariantCallingMethods.CUTESV:
         return VariantCallingMethods.AttributeTypes.CUTESV
     elif variant_calling_method == VariantCallingMethods.DEEPVARIANT:
         return VariantCallingMethods.AttributeTypes.DEEPVARIANT