Add new Genotype methods hasRefAllele and hasAltAllele (#1678)

samtools · Aug 8, 2023 · 1e5ec5a · 1e5ec5a
1 parent 20334af
commit 1e5ec5a
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Showing 3 changed files with 40 additions and 0 deletions.
diff --git a/src/main/java/htsjdk/variant/variantcontext/Allele.java b/src/main/java/htsjdk/variant/variantcontext/Allele.java
@@ -431,5 +431,8 @@ static boolean oneIsPrefixOfOther(final Allele a1, final Allele a2) {
 
     int length();
 
+    /**
+     *  @return true if Allele is either {@code <NON_REF>} or {@code <*>}
+     */
     boolean isNonRefAllele();
 }
diff --git a/src/main/java/htsjdk/variant/variantcontext/Genotype.java b/src/main/java/htsjdk/variant/variantcontext/Genotype.java
@@ -77,6 +77,20 @@ protected Genotype(final String sampleName, final String filters) {
      */
     public abstract List<Allele> getAlleles();
 
+    /**
+     * @return true if any allele is REF
+     */
+    public boolean hasRefAllele() {
+        return getAlleles().stream().anyMatch(A->A.isReference());
+    };
+
+    /**
+     * @return true if any allele is ALT, (NO_CALL are ignored)
+     */
+    public boolean hasAltAllele() {
+        return getAlleles().stream().anyMatch(A->!(A.isReference() || A.isNoCall()));
+    };
+
     /**
      * Returns how many times allele appears in this genotype object?
      *

diff --git a/src/test/java/htsjdk/variant/variantcontext/GenotypeUnitTest.java b/src/test/java/htsjdk/variant/variantcontext/GenotypeUnitTest.java
@@ -31,6 +31,7 @@
 
 import htsjdk.variant.VariantBaseTest;
 import htsjdk.variant.vcf.VCFConstants;
+import java.util.Arrays;
 import org.testng.Assert;
 import org.testng.annotations.BeforeSuite;
 import org.testng.annotations.Test;
@@ -70,6 +71,28 @@ public void testFilters() {
         Assert.assertFalse(makeGB().filter("").make().isFiltered(), "empty filters should count as unfiltered");
         Assert.assertEquals(makeGB().filter("").make().getFilters(), null, "empty filter string should result in null filters");
     }
+
+    @Test
+    public void testHasAltAllele() {
+        Assert.assertTrue(GenotypeBuilder.create("s", Arrays.asList(A)).hasAltAllele());
+        Assert.assertTrue(GenotypeBuilder.create("s", Arrays.asList(A,Aref)).hasAltAllele());
+        Assert.assertTrue(GenotypeBuilder.create("s", Arrays.asList(A,Allele.NO_CALL)).hasAltAllele());
+        Assert.assertFalse(GenotypeBuilder.create("s", Arrays.asList(Aref)).hasAltAllele());
+        Assert.assertFalse(GenotypeBuilder.create("s", Arrays.asList(Aref,Aref)).hasAltAllele());
+        Assert.assertFalse(GenotypeBuilder.create("s", Arrays.asList(Allele.NO_CALL,Allele.NO_CALL)).hasAltAllele());
+        Assert.assertTrue(GenotypeBuilder.create("s", Arrays.asList(Allele.NON_REF_ALLELE)).hasAltAllele());
+        Assert.assertTrue(GenotypeBuilder.create("s", Arrays.asList(Allele.SPAN_DEL)).hasAltAllele());
+    }
+
+    @Test
+    public void testHasRefAllele() {
+        Assert.assertFalse(GenotypeBuilder.create("s", Arrays.asList(A)).hasRefAllele());
+        Assert.assertTrue(GenotypeBuilder.create("s", Arrays.asList(A,Aref)).hasRefAllele());
+        Assert.assertFalse(GenotypeBuilder.create("s", Arrays.asList(A,Allele.NO_CALL)).hasRefAllele());
+        Assert.assertTrue(GenotypeBuilder.create("s", Arrays.asList(Aref)).hasRefAllele());
+        Assert.assertTrue(GenotypeBuilder.create("s", Arrays.asList(Aref,Aref)).hasRefAllele());
+        Assert.assertFalse(GenotypeBuilder.create("s", Arrays.asList(Allele.NO_CALL,Allele.NO_CALL)).hasRefAllele());
+    }
 
 //    public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean isPhased) {
 //    public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean isPhased, double[] log10Likelihoods) {