Added -trimAlternates argument to SelectVariants

* PT 84021222
 * -trimAlternates removes all unused alternate alleles from variants.  Note that this is pretty aggressive for monomorphic sites

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java

@@ -53,8 +53,10 @@ package org.broadinstitute.gatk.tools.walkers.variantutils;
 
 import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
+import java.io.File;
 import java.util.Arrays;
 
 public class SelectVariantsIntegrationTest extends WalkerTest {
@@ -280,7 +282,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         String testFile = privateTestDir + "vcfexample.loseAlleleInSelection.vcf";
 
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-T SelectVariants --keepOriginalAC -env -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
+                "-T SelectVariants --keepOriginalAC -env -trimAlternates -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
                 Arrays.asList("4695c99d96490ed4e5b1568c5b52dea6")
         );
@@ -319,7 +321,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         String testfile = privateTestDir + "multi-allelic.bi-allelicInGIH.vcf";
         String samplesFile = privateTestDir + "GIH.samples.list";
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header -sf " + samplesFile + " --excludeNonVariants --variant " + testfile,
+                "-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header -sf " + samplesFile + " --excludeNonVariants -trimAlternates --variant " + testfile,
                 1,
                 Arrays.asList("69862fb97e8e895fe65c7abb14b03cee")
         );
@@ -382,8 +384,35 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
     @Test
     public void testAlleleTrimming() {
         final String testFile = privateTestDir + "forHardLeftAlignVariantsTest.vcf";
-        final String cmd = "-T SelectVariants -R " + b36KGReference + " -sn NA12878 -env "
-                + testFile + " -o %s --no_cmdline_in_header";
-        WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("69c3f59c132418ec10117aa395addfea"));
+        final String cmd = "-T SelectVariants -R " + b37KGReference + " -sn NA12878 -env -trimAlternates "
+                + "-V " + testFile + " -o %s --no_cmdline_in_header";
+        WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("9df942000eb18b12d9008c7d9b5c4178"));
+        executeTest("testAlleleTrimming", spec);
+    }
+
+    @DataProvider(name="unusedAlleleTrimmingProvider")
+    public Object[][] unusedAlleleTrimmingProvider() {
+        return new Object[][] {
+                { privateTestDir+"forHardLeftAlignVariantsTest.vcf", "-trimAlternates", "9df942000eb18b12d9008c7d9b5c4178"},
+                { privateTestDir+"forHardLeftAlignVariantsTest.vcf", "", "981b757e3dc6bf3864ac7e493cf9d30d"},
+                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT", "8ded359dd87fd498ff38736ea0fa4c28"},
+                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env", "a7e7288dcd779cfac6983069de45b79c"},
+                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -trimAlternates", "2e726d06a8d317199e8dda74691948a3"},
+                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env -trimAlternates", "1e5585f86c347da271a79fbfc61ac849"}
+        };
+    }
+
+    @Test(dataProvider = "unusedAlleleTrimmingProvider")
+    public void testUnusedAlleleTrimming(final String vcf, final String extraArgs, final String md5) {
+        final WalkerTestSpec spec = new WalkerTestSpec(
+                "-T SelectVariants" +
+                        " -R "+b37KGReference +
+                        " -V "+vcf +
+                        " -o %s --no_cmdline_in_header" +
+                        " "+extraArgs,
+                1,
+                Arrays.asList(md5)
+        );
+        executeTest(String.format("testUnusedAlleleTrimming: (%s,%s)", new File(vcf).getName(), extraArgs), spec);
     }
 }

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java

@@ -99,7 +99,7 @@ public class SelectVariantsParallelIntegrationTest extends WalkerTest {
             }
             { // AD and PL decoding race condition
                 final String testfile = privateTestDir + "race_condition.vcf";
-                final String args = "-env -sn SAMPLE -L 1:1-10,000,000 -V " + testfile;
+                final String args = "-env -trimAlternates -sn SAMPLE -L 1:1-10,000,000 -V " + testfile;
                 new ParallelSelectTestProvider(b37KGReference, args, "e86c6eb105ecdd3ff026999ffc692821", nt);
             }
         }

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java

@@ -253,6 +253,15 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
     @Argument(fullName="preserveAlleles", shortName="noTrim", doc="Preserve original alleles, do not trim", required=false)
     protected boolean preserveAlleles = false;
 
+    /**
+     * When this argument is present, all alternate alleles that are not present in the (output) samples will be removed.
+     * Note that this even extends to biallelic SNPs - if the alternate allele is not present in any sample, it will be
+     * removed and the record will contain a '.' in the ALT column.  Also note that sites-only VCFs, by definition, do
+     * not include the alternate allele in any genotype calls.
+     */
+    @Argument(fullName="removeUnusedAlternates", shortName="trimAlternates", doc="Remove alternate alleles not present in any genotypes", required=false)
+    protected boolean removeUnusedAlternates = false;
+
     /**
      * When this argument is used, we can choose to include only multiallelic or biallelic sites, depending on how many alleles are listed in the ALT column of a vcf.
      * For example, a multiallelic record such as:
@@ -528,7 +537,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
             if ( containsIndelLargerThan(vc, maxIndelSize) )
                 continue;
 
-            VariantContext sub = subsetRecord(vc, EXCLUDE_NON_VARIANTS, preserveAlleles);
+            VariantContext sub = subsetRecord(vc, preserveAlleles, removeUnusedAlternates);
 
             if ( (!EXCLUDE_NON_VARIANTS || sub.isPolymorphicInSamples()) && (!EXCLUDE_FILTERED || !sub.isFiltered()) ) {
                 boolean failedJexlMatch = false;
@@ -681,25 +690,30 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
      * Helper method to subset a VC record, modifying some metadata stored in the INFO field (i.e. AN, AC, AF).
      *
      * @param vc       the VariantContext record to subset
-     * @param excludeNonVariants should we exclude sites that have AC=0 for any alternate alleles?
+     * @param preserveAlleles should we trim constant sequence from the beginning and/or end of all alleles, or preserve it?
+     * @param removeUnusedAlternates removes alternate alleles with AC=0
      * @return the subsetted VariantContext
      */
-    private VariantContext subsetRecord(final VariantContext vc, final boolean excludeNonVariants, final boolean preserveAlleles) {
-        if ( NO_SAMPLES_SPECIFIED || samples.isEmpty() )
+    private VariantContext subsetRecord(final VariantContext vc, final boolean preserveAlleles, final boolean removeUnusedAlternates) {
+        //subContextFromSamples() always decodes the vc, which is a fairly expensive operation.  Avoid if possible
+        if ( NO_SAMPLES_SPECIFIED && !removeUnusedAlternates )
             return vc;
 
-        final VariantContext sub = vc.subContextFromSamples(samples, excludeNonVariants); // strip out the alternate alleles that aren't being used
+        // strip out the alternate alleles that aren't being used
+        final VariantContext sub = vc.subContextFromSamples(samples, removeUnusedAlternates);
+
+        //If no subsetting happened, exit now
+        if ( sub.getNSamples() == vc.getNSamples() && sub.getNAlleles() == vc.getNAlleles() )
+            return vc;
 
         final VariantContextBuilder builder = new VariantContextBuilder(sub);
 
         // if there are fewer alternate alleles now in the selected VC, we need to fix the PL and AD values
         GenotypesContext newGC = GATKVariantContextUtils.updatePLsAndAD(sub, vc);
 
-        // if we have fewer samples in the selected VC than in the original VC, we need to strip out the MLE tags
-        if ( vc.getNSamples() != sub.getNSamples() ) {
-            builder.rmAttribute(GATKVCFConstants.MLE_ALLELE_COUNT_KEY);
-            builder.rmAttribute(GATKVCFConstants.MLE_ALLELE_FREQUENCY_KEY);
-        }
+        // since the VC has been subset (either by sample or allele), we need to strip out the MLE tags
+        builder.rmAttribute(GATKVCFConstants.MLE_ALLELE_COUNT_KEY);
+        builder.rmAttribute(GATKVCFConstants.MLE_ALLELE_FREQUENCY_KEY);
 
         // Remove a fraction of the genotypes if needed
         if ( fractionGenotypes > 0 ){