analysis: implement the variant sample stats tranformer, #20

opencb · Sep 23, 2019 · b831876 · b831876
1 parent 45f59b2
commit b831876
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Showing 5 changed files with 1,013 additions and 11 deletions.
diff --git a/...va/org/opencb/oskar/spark/variant/analysis/transformers/ModeOfInheritanceTransformer.java b/...va/org/opencb/oskar/spark/variant/analysis/transformers/ModeOfInheritanceTransformer.java
@@ -6,6 +6,7 @@
 import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Row;
 import org.apache.spark.sql.catalyst.expressions.ArrayContains;
+import org.opencb.biodata.models.clinical.interpretation.ClinicalProperty;
 import org.opencb.biodata.models.clinical.pedigree.Pedigree;
 import org.opencb.biodata.models.commons.Disorder;
 import org.opencb.biodata.tools.pedigree.ModeOfInheritance;
@@ -123,6 +124,9 @@ public Dataset<Row> transform(Dataset<?> dataset) {
         String phenotype = getPhenotype();
         String studyId = getStudyId();
         Boolean incompletePenetrance = getOrDefault(incompletePenetranceParam);
+        ClinicalProperty.Penetrance penetrance = getOrDefault(incompletePenetranceParam)
+                ? ClinicalProperty.Penetrance.INCOMPLETE
+                : ClinicalProperty.Penetrance.COMPLETE;
         Boolean missingAsReference = getOrDefault(missingAsReferenceParam);
 
         Map<String, List<String>> samplesMap = vmm.samples(df);
@@ -142,22 +146,22 @@ public Dataset<Row> transform(Dataset<?> dataset) {
         switch (moiLowerCase) {
             case MONOALLELIC:
             case "dominant":
-                gtsMap = ModeOfInheritance.dominant(pedigree, disorder, incompletePenetrance);
+                gtsMap = ModeOfInheritance.dominant(pedigree, disorder, penetrance);
                 break;
             case BIALLELIC:
             case "recessive":
-                gtsMap = ModeOfInheritance.recessive(pedigree, disorder, incompletePenetrance);
+                gtsMap = ModeOfInheritance.recessive(pedigree, disorder, penetrance);
                 break;
             case X_LINKED_MONOALLELIC_INTERNAL: // Internal values already in lower case
-                gtsMap = ModeOfInheritance.xLinked(pedigree, disorder, true);
+                gtsMap = ModeOfInheritance.xLinked(pedigree, disorder, true, penetrance);
                 df = df.filter(df.col("chromosome").equalTo("X"));
                 break;
             case X_LINKED_BIALLELIC_INTERNAL: // Internal values already in lower case
-                gtsMap = ModeOfInheritance.xLinked(pedigree, disorder, false);
+                gtsMap = ModeOfInheritance.xLinked(pedigree, disorder, false, penetrance);
                 df = df.filter(df.col("chromosome").equalTo("X"));
                 break;
             case Y_LINKED_INTERNAL: // Internal values already in lower case
-                gtsMap = ModeOfInheritance.yLinked(pedigree, disorder);
+                gtsMap = ModeOfInheritance.yLinked(pedigree, disorder, penetrance);
                 df = df.filter(df.col("chromosome").equalTo("Y"));
                 break;
             default: