updating ArrayCalculateMetrics for new genotype counts table (#6843)

broadinstitute · Sep 22, 2020 · 889c38f · 889c38f
1 parent c79cd40
commit 889c38f
Show file tree

Hide file tree

Showing 2 changed files with 23 additions and 7 deletions.
diff --git a/...main/java/org/broadinstitute/hellbender/tools/variantdb/arrays/ArrayCalculateMetrics.java b/...main/java/org/broadinstitute/hellbender/tools/variantdb/arrays/ArrayCalculateMetrics.java
@@ -44,7 +44,7 @@ public class ArrayCalculateMetrics extends GATKTool {
 
     public enum HeaderFieldEnum {
         probe_id,
-        hwe_pval,
+        excess_het,
         call_rate,
         invariant
     }
@@ -72,14 +72,19 @@ public void traverse() {
             for ( final GenericRecord row : reader ) {
                 List<String> thisRow = new ArrayList<>();
                 // data in row should never be null
-                long probeId = (Long) row.get(0);
+                long probeId = (Long) row.get(GenotypeCountsSchema.PROBE_ID_INDEX);
                 thisRow.add(String.valueOf(probeId));
 
-                GenotypeCounts genotypeCounts = new GenotypeCounts((Long) row.get(1), (Long) row.get(2), (Long) row.get(3));
-                long noCalls = (Long) row.get(4);
+                long combined_hom_var = (Long) row.get(GenotypeCountsSchema.HOM_VAR_INDEX) +
+                        (Long) row.get(GenotypeCountsSchema.HET_1_2_INDEX) +
+                        (Long) row.get(GenotypeCountsSchema.HOM_VAR_2_2_INDEX);
+
+                GenotypeCounts genotypeCounts = new GenotypeCounts((Long) row.get(GenotypeCountsSchema.HOM_REF_INDEX),
+                        (Long) row.get(GenotypeCountsSchema.HET_INDEX), combined_hom_var);
+                long noCalls = (Long) row.get(GenotypeCountsSchema.NO_CALL_INDEX);
                 int sampleCount = (int) genotypeCounts.getRefs() + (int) genotypeCounts.getHets() + (int) genotypeCounts.getHoms() + (int) noCalls;
-                double excessHetPval = ExcessHet.calculateEH(genotypeCounts, sampleCount).getRight();
-                thisRow.add(String.format("%.0f", excessHetPval));
+                double excessHet = ExcessHet.calculateEH(genotypeCounts, sampleCount).getRight();
+                thisRow.add(String.format("%.0f", excessHet));
 
                 double callRate = 1.0 - ((double) noCalls / sampleCount);
                 thisRow.add(String.format("%.3f", callRate));

diff --git a/...ava/org/broadinstitute/hellbender/tools/variantdb/arrays/tables/GenotypeCountsSchema.java b/...ava/org/broadinstitute/hellbender/tools/variantdb/arrays/tables/GenotypeCountsSchema.java
@@ -9,7 +9,18 @@ public class GenotypeCountsSchema {
     public static final String HOM_REF_COUNT = "hom_ref";
     public static final String HET_COUNT = "het";
     public static final String HOM_VAR_COUNT = "hom_var";
+    public static final String HET_1_2_COUNT = "het_1_2";
+    public static final String HOM_VAR_2_2_COUNT = "hom_var_2_2";
     public static final String NO_CALL_COUNT = "no_call";
 
-    public static final List<String> GENOTYPE_COUNTS_FIELDS = Arrays.asList(PROBE_ID, HOM_REF_COUNT, HET_COUNT, HOM_VAR_COUNT, NO_CALL_COUNT);
+    public static final int PROBE_ID_INDEX = 0;
+    public static final int HOM_REF_INDEX = 1;
+    public static final int HET_INDEX = 2;
+    public static final int HOM_VAR_INDEX = 3;
+    public static final int HET_1_2_INDEX = 4;
+    public static final int HOM_VAR_2_2_INDEX = 5;
+    public static final int NO_CALL_INDEX = 6;
+
+
+    public static final List<String> GENOTYPE_COUNTS_FIELDS = Arrays.asList(PROBE_ID, HOM_REF_COUNT, HET_COUNT, HOM_VAR_COUNT, HET_1_2_COUNT, HOM_VAR_2_2_COUNT, NO_CALL_COUNT);
 }