Added warning for unsorted genotype field

src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariants.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.hellbender.tools.walkers.variantutils;
 
 import htsjdk.samtools.SAMSequenceDictionary;
+import htsjdk.tribble.util.ParsingUtils;
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.Genotype;
 import htsjdk.variant.variantcontext.GenotypeBuilder;
@@ -420,6 +421,11 @@ public final class SelectVariants extends VariantWalker {
             doc="Suppress reference path in output for test result differencing")
     private boolean suppressReferencePath = false;
 
+    @Hidden
+    @Argument(fullName="fail-on-unsorted-genotype", optional=true,
+            doc="Throw an exception if the genotype field is unsorted")
+    private boolean failOnUnsortedGenotype = false;
+
     @ArgumentCollection
     private GenomicsDBArgumentCollection genomicsdbArgs = new GenomicsDBArgumentCollection();
 
@@ -472,6 +478,21 @@ protected GenomicsDBOptions getGenomicsDBOptions() {
     public void onTraversalStart() {
         final Map<String, VCFHeader> vcfHeaders = Collections.singletonMap(getDrivingVariantsFeatureInput().getName(), getHeaderForVariants());
 
+        final List<String> genotypeField = getHeaderForVariants().getGenotypeSamples();
+        if(!ParsingUtils.isSorted(genotypeField)){
+            if(genotypeField.size() > 10) {
+                logger.warn("***************************************************************************************************************************");
+                logger.warn("* Detected unsorted genotype fields on input.                                                                             *");
+                logger.warn("* SelectVariants will sort the genotypes on output which could result in slow traversal as it involves genotype parsing.  *");
+                logger.warn("***************************************************************************************************************************");
+            }
+            if(failOnUnsortedGenotype){
+                throw new UserException.ValidationFailure("Input file genotypes are unsorted and we are in strict genotype ordering validation mode.");
+            }
+        }
+
+
+
         // Initialize VCF header lines
         final Set<VCFHeaderLine> headerLines = createVCFHeaderLineList(vcfHeaders);
 

src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/SelectVariantsIntegrationTest.java

@@ -67,6 +67,20 @@ public void testExpressionSelection() throws IOException {
         spec.executeTest("testSimpleExpressionSelection--" + testFile, this);
     }
 
+    @Test(expectedExceptions = UserException.ValidationFailure.class)
+    public void testResortingFileWarning() throws IOException {
+        final String testFile = getToolTestDataDir() + "unsortedGenotypeFieldsTestFile.vcf";
+        final File output = File.createTempFile("test_unsortedGenotypeField", ".vcf");
+
+        final ArgumentsBuilder args = new ArgumentsBuilder()
+                .addVCF(testFile)
+                .addOutput(output)
+                .addFlag("fail-on-unsorted-genotype");
+
+        runCommandLine(args);
+
+    }
+
     @Test
     public void testRepeatedLineSelectionAndExludeFiltered() throws IOException {
         final String testFile = getToolTestDataDir() + "test.dup.vcf";