From 9aa70d9c7cee7240241cc327055be0df48fb6f6b Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 8 Aug 2010 07:07:42 +0000
Subject: [PATCH] Replaced by SelectVariants

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3979 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/vcftools/VariantSubset.java  | 106 ------------------
 1 file changed, 106 deletions(-)
 delete mode 100755 java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSubset.java

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSubset.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSubset.java
deleted file mode 100755
index 496ecf75d..000000000
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSubset.java
+++ /dev/null
@@ -1,106 +0,0 @@
-/*
- * Copyright (c) 2010.
- *
- * 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.playground.gatk.walkers.vcftools;
-
-import org.broad.tribble.util.variantcontext.Genotype;
-import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broad.tribble.vcf.VCFHeader;
-import org.broad.tribble.vcf.VCFHeaderLine;
-
-import java.util.*;
-
-/**
- * Extracts subsets of a VCF file like one or more samples, all or only variant loci, all or filtered loci.
- */
-public class VariantSubset extends RodWalker<Integer, Integer> {
-    @Argument(fullName="sample", shortName="SN", doc="Sample to include (or nothing to specify all samples)", required=false)
-    private ArrayList<String> SAMPLES = null;
-
-    @Argument(fullName="includeNonVariants", shortName="INV", doc="Include non-variant loci", required=false)
-    private boolean INCLUDE_NON_VARIANTS = false;
-
-    @Argument(fullName="includeFiltered", shortName="IF", doc="Include filtered loci", required=false)
-    private boolean INCLUDE_FILTERED = false;
-
-    private VCFWriter writer;
-
-    public void initialize() {
-        Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
-        metaData.add(new VCFHeaderLine("source", "VariantsToVCF"));
-        metaData.add(new VCFHeaderLine("reference", this.getToolkit().getArguments().referenceFile.getAbsolutePath()));
-
-        writer = new VCFWriter(out);
-        Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList("variant"));
-
-        final VCFHeader vcfHeader = new VCFHeader(metaData, samples);
-        writer.writeHeader(vcfHeader);
-    }
-
-    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        Collection<VariantContext> VCs = tracker.getAllVariantContexts(ref, null, context.getLocation(), true, false);
-        for (VariantContext vc : VCs) {
-            VariantContext subset = subsetRecord(vc);
-
-            if ( (vc.isPolymorphic() || INCLUDE_NON_VARIANTS) &&
-                    (!subset.isFiltered() || INCLUDE_FILTERED) )
-                writer.add(subset, ref.getBase());
-        }
-
-        return 1;
-    }
-
-    public Integer reduceInit() {
-        return 0;
-    }
-
-    private VariantContext subsetRecord(VariantContext vc) {
-        if ( SAMPLES == null || SAMPLES.isEmpty() )
-            return vc;
-
-        ArrayList<Genotype> genotypes = new ArrayList<Genotype>();
-        for ( Map.Entry<String, Genotype> genotypePair : vc.getGenotypes().entrySet() ) {
-            if ( SAMPLES.contains(genotypePair.getKey()) )
-                genotypes.add(genotypePair.getValue());
-        }
-
-        return vc.subContextFromGenotypes(genotypes);
-    }
-
-    public Integer reduce(Integer sum, Integer value) {
-        return 1;
-    }
-
-    public void onTraversalDone(Integer sum) {
-        writer.close();
-    }
-}