Mask snps with --snpmask

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceIntegrationTest.java

@@ -115,13 +115,33 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
     }
 
     @Test
-    public void testIndelsAndSnpMask() {
+    public void testSnpMask() {
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + b36dbSNP129 + " --snpmask:vcf " + b36dbSNP129 + " -L 1:10,271,272-10,271,302 -o %s",
+                1,
+                Arrays.asList("01a0dffc62fc940c97e29276457f1ff0"));
+        executeTest("test snp mask", spec);
+    }
+
+    @Test
+    public void testSnpMaskPriority() {
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + b36dbSNP129 + " --snpmaskPriority --snpmask:vcf " + b36dbSNP129 + " -L 1:10,271,272-10,271,302 -o %s",
+                1,
+                Arrays.asList("0950493e5038f7d588034ce4dd21292a"));
+        executeTest("test snp mask priority", spec);
+    }
+
+    @Test
+         public void testIndelsAndSnpMask() {
 
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 --snpmask:vcf " + b36dbSNP129 + " -L 1:10,075,000-10,075,380 -L 1:10,093,447-10,093,847 -L 1:10,271,252-10,271,452 -o %s",
-                 1,
+                1,
-                 Arrays.asList("375efb2feb017f01339f680fdffac6cd"));
+                Arrays.asList("375efb2feb017f01339f680fdffac6cd"));
-        executeTest("test indels", spec);
+        executeTest("test indels and snp mask", spec);
     }
 
     @Test

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceMaker.java

@@ -102,12 +102,17 @@ public class FastaAlternateReferenceMaker extends FastaReferenceMaker {
     protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
 
     /**
-     * Snps from this file are used as a mask (inserting N's in the sequence) when constructing the alternate reference
+     * SNPs from this file are used as a mask (inserting N's in the sequence) when constructing the alternate reference
-     * (regardless of whether they overlap a variant site).
      */
     @Input(fullName="snpmask", shortName = "snpmask", doc="SNP mask VCF file", required=false)
     protected RodBinding<VariantContext> snpmask;
 
+    /**
+     * Gives priority to a SNP mask over an input VCF for a site. Only has an effect if the --snpmask argument is used.
+     */
+    @Argument(fullName="snpmaskPriority", shortName = "snpmaskPriority", doc="SNP mask priority", required=false)
+    protected Boolean snpmaskPriority = false;
+
     /**
      * This option will generate an error if the specified sample does not exist in the VCF.
      * Non-diploid (or non-called) genotypes are ignored.
@@ -138,6 +143,13 @@ public class FastaAlternateReferenceMaker extends FastaReferenceMaker {
 
         final String refBase = String.valueOf((char)ref.getBase());
 
+        // If we have a mask at this site, use it
+        if ( snpmaskPriority ){
+            final Pair<GenomeLoc, String> mask = maskSnp(tracker, context);
+            if ( mask != null )
+                return mask;
+        }
+
         // Check to see if we have a called snp
         for ( final VariantContext vc : tracker.getValues(variantCollection.variants, ref.getLocus()) ) {
             if ( vc.isFiltered() )
@@ -155,17 +167,33 @@ public class FastaAlternateReferenceMaker extends FastaReferenceMaker {
             }
         }
 
-        // if we don't have a called site, and we have a mask at this site, mask it
+        if ( !snpmaskPriority ){
-        for ( final VariantContext vc : tracker.getValues(snpmask) ) {
+            final Pair<GenomeLoc, String> mask = maskSnp(tracker, context);
-            if ( vc.isSNP()) {
+            if ( mask != null )
-                return new Pair<>(context.getLocation(), "N");
+                return mask;
-            }
         }
 
         // if we got here then we're just ref
         return new Pair<>(context.getLocation(), refBase);
     }
 
+    /**
+     * Mask a SNP (inserting N's in the sequence)
+     *
+     * @param tracker the Reference Metadata available at a particular site in the genome
+     * @param context the locus context data
+     * @return mask at the locus or null if no SNP at that locus
+     */
+    private Pair<GenomeLoc, String> maskSnp(final RefMetaDataTracker tracker, final AlignmentContext context){
+        for (final VariantContext vc : tracker.getValues(snpmask)) {
+            if (vc.isSNP()) {
+                return new Pair<>(context.getLocation(), "N");
+            }
+        }
+
+        return null;
+    }
+
     /**
      * Returns the IUPAC encoding for the given genotype or the reference base if not possible
      *