VCF codec should handle multiple missing GL fields (#1372)

* VCF codec should handle multiple missing GL fields * throw error for partial missing values for GL field
samtools · Jun 17, 2019 · b804a47 · b804a47
1 parent 58199e6
commit b804a47
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Showing 2 changed files with 27 additions and 3 deletions.
diff --git a/src/main/java/htsjdk/variant/variantcontext/GenotypeLikelihoods.java b/src/main/java/htsjdk/variant/variantcontext/GenotypeLikelihoods.java
@@ -242,7 +242,7 @@ public static double getGQLog10FromLikelihoods(int iOfChoosenGenotype, double[]
     }
 
     private final static double[] parsePLsIntoLikelihoods(String likelihoodsAsString_PLs) {
-        if ( !likelihoodsAsString_PLs.equals(VCFConstants.MISSING_VALUE_v4) ) {
+        if ( likelihoodsAsString_PLs != null && !likelihoodsAsString_PLs.equals(VCFConstants.MISSING_VALUE_v4) ) {
             String[] strings = likelihoodsAsString_PLs.split(",");
             double[] likelihoodsAsVector = new double[strings.length];
             try {
@@ -266,10 +266,21 @@ private final static double[] parseDeprecatedGLString(String GLString) {
         if ( !GLString.equals(VCFConstants.MISSING_VALUE_v4) ) {
             String[] strings = GLString.split(",");
             double[] likelihoodsAsVector = new double[strings.length];
+            int missing = 0;
             for ( int i = 0; i < strings.length; i++ ) {
-                likelihoodsAsVector[i] = Double.parseDouble(strings[i]);
+                if (strings[i].equals(VCFConstants.MISSING_VALUE_v4)) {
+                  missing++;
+                } else {
+                  likelihoodsAsVector[i] = Double.parseDouble(strings[i]);
+                }
+            }
+            if (missing == 0) {
+              return likelihoodsAsVector;
+            } else if (likelihoodsAsVector.length == missing) {
+              return null; // array of missing values 
+            } else {
+              throw new TribbleException("partial missing values for GL field");
             }
-            return likelihoodsAsVector;
         }
 
         return null;

diff --git a/src/test/java/htsjdk/variant/variantcontext/GenotypeLikelihoodsUnitTest.java b/src/test/java/htsjdk/variant/variantcontext/GenotypeLikelihoodsUnitTest.java
@@ -82,6 +82,19 @@ public void testFromString2() {
         Assert.assertEquals(gl.getAsString(), vPLString);
     }
 
+    @Test
+    public void testFromStringMultipleMissing() {
+        String missingWithPloidy2AltAllele1 = ".,.,.";
+        GenotypeLikelihoods gl = GenotypeLikelihoods.fromGLField(missingWithPloidy2AltAllele1);
+        Assert.assertNull(gl.getAsPLs());
+    }
+
+    @Test (expectedExceptions = TribbleException.class)
+    public void testFromStringOneMissing() {
+        String oneMissingFromPloidy2AltAllele1 = "-3.0,.,-1.2";
+        GenotypeLikelihoods.fromGLField(oneMissingFromPloidy2AltAllele1);
+    }
+
     @Test (expectedExceptions = TribbleException.class)
     public void testErrorBadFormat() {
         GenotypeLikelihoods gl = GenotypeLikelihoods.fromPLField("adf,b,c");