Merge pull request #448 from broadinstitute/eb_add_stuff_to_the_bundle

Eb add stuff to the bundle

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java

@@ -77,32 +77,49 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
         writer.writeHeader(vcfHeader);
     }
 
-    private void filterAndWrite(byte[] ref, VariantContext vc) {
+    /**
+     * Determines whether records should be filtered; if not, writes them to the output
+     *
+     * @param ref   the reference context
+     * @param vc    the VariantContext to process
+     * @return true if the record is not filtered, false otherwise
+     */
+    protected boolean filterOrWrite(final byte[] ref, final VariantContext vc) {
+	if ( ref == null ) throw new IllegalArgumentException("Cannot filter based on a null reference array");
+	if ( vc == null ) throw new IllegalArgumentException("Cannot filter a null Variant Context");
 
         totalLocs++;
 
-        boolean failed = false;
+        boolean filter = false;
-        byte[] recordRef = vc.getReference().getBases();
+        final byte[] recordRef = vc.getReference().getBases();
-        for (int i = 0; i < recordRef.length && i < MAX_VARIANT_SIZE; i++) {
+
-            if ( recordRef[i] != ref[i] ) {
+        // this can happen for records that get placed at the ends of chromosomes
-                failed = true;
+        if ( recordRef.length > ref.length ) {
-                break;
+            filter = true;
+        } else {
+            for (int i = 0; i < recordRef.length && i < MAX_VARIANT_SIZE; i++) {
+                if ( recordRef[i] != ref[i] ) {
+                    filter = true;
+                    break;
+                }
             }
         }
 
-        if ( failed )
+        if ( filter )
             failedLocs++;
         else
             writer.add(vc);
+
+        return !filter;
     }
 
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         if ( tracker == null )
             return 0;
 
-        Collection<VariantContext> VCs = tracker.getValues(variantCollection.variants, context.getLocation());
+        final Collection<VariantContext> VCs = tracker.getValues(variantCollection.variants, context.getLocation());
-        for ( VariantContext vc : VCs )
+        for ( final VariantContext vc : VCs )
-            filterAndWrite(ref.getBases(), vc);
+            filterOrWrite(ref.getBases(), vc);
 
         return 0;
     }
@@ -114,4 +131,4 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
     public void onTraversalDone(Integer result) {
         System.out.println("Filtered " + failedLocs + " records out of " + totalLocs + " total records.");
     }
-}
+}

public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariantsUnitTest.java

@@ -0,0 +1,54 @@
+/*
+* Copyright (c) 2012 The Broad Institute
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.sting.gatk.walkers.variantutils;
+
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.util.ArrayList;
+import java.util.List;
+
+
+public class FilterLiftedVariantsUnitTest extends BaseTest {
+
+    @Test
+    public void testIndelAtEndOfContig() {
+
+        final List<Allele> alleles = new ArrayList<>(2);
+        alleles.add(Allele.create("AAAAA", true));
+        alleles.add(Allele.create("A", false));
+        final VariantContext vc = new VariantContextBuilder("test", "1", 10, 14, alleles).make();
+
+        final FilterLiftedVariants filter = new FilterLiftedVariants();
+
+        Assert.assertFalse(filter.filterOrWrite(new byte[]{'A'}, vc));
+    }
+
+}

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala

@@ -168,11 +168,18 @@ class GATKResourcesBundle extends QScript {
       "Mills_and_1000G_gold_standard.indels", b37, true, false))
 
     //
-    // CEU trio (NA12878,NA12891,NA12892) best practices results (including PBT)
+    // CEU trio (NA12878,NA12891,NA12892) best practices results
     //
 
-    addResource(new Resource("/humgen/gsa-hpprojects/NA12878Collection/callsets/CEUtrio_BestPractices/CEUTrio.HiSeq.WGS.b37.snps_and_indels.recalibrated.filtered.phased.CURRENT.vcf",
+    addResource(new Resource("/humgen/1kg/processing/production_wgs_final/trio/CEU/CEU.wgs.HaplotypeCaller.20131118.snps_indels.high_coverage_pcr_free.genotypes.vcf",
-      "CEUTrio.HiSeq.WGS.b37.bestPractices.phased",b37,true,false))
+      "CEUTrio.HiSeq.WGS.b37.bestPractices",b37,true,false))
+
+    //
+    // NA12878 knowledgebase snapshot
+    //
+
+    addResource(new Resource("/humgen/gsa-hpprojects/NA12878Collection/knowledgeBase/snapshots/NA12878.wgs.broad_truth_set.20131119.snps_and_indels.genotypes.vcf",
+      "NA12878.knowledgebase.snapshot.20131119",b37,true,false))
 
     //
     // example call set for documentation guide tutorial
@@ -290,9 +297,8 @@ class GATKResourcesBundle extends QScript {
         }
       }
 
-      createCurrentLink(BUNDLE_DIR)
-
     } else {
+      createCurrentLink(BUNDLE_DIR)
       createBundleDirectories(DOWNLOAD_DIR)
       createDownloadsFromBundle(BUNDLE_DIR, DOWNLOAD_DIR)
     }