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Moving VariantsToVCF to the proper directory; removing the oneoffs CG indel converter in preparation for a ligitimate CG variant Feature class in the works. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5207 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-02-07 05:21:01 +00:00
parent 35c688ac67
commit 698096dc5a
3 changed files with 3 additions and 188 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java → java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
View File

@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers;
package org.broadinstitute.sting.gatk.walkers.variantutils;
import net.sf.samtools.util.CloseableIterator;
import org.broad.tribble.dbsnp.DbSNPCodec;
@ -43,6 +43,7 @@ import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.BaseUtils;

186
java/src/org/broadinstitute/sting/oneoffprojects/walkers/CGIndelConverter.java
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@ -1,186 +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.oneoffprojects.walkers;
import org.broad.tribble.readers.AsciiLineReader;
import org.broad.tribble.util.variantcontext.Allele;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.*;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
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.RefWalker;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.*;
/**
* Converts CG indels to VCF format
*/
public class CGIndelConverter extends RefWalker<Integer, Integer> {
@Output(doc="File to which variants should be written",required=true)
protected VCFWriter writer = null;
@Argument(fullName="raw_cg_rod_file", shortName="cg", doc="file with raw cg calls", required=true)
private File CG_FILE = null;
@Argument(fullName="sample_name", shortName="sample", doc="sample represented by the calls", required=true)
private String sample = null;
private HashMap<String, IndelCall> calls = new HashMap<String, IndelCall>();
private static class IndelCall {
public String chr, pos, bases, type, id;
public int count;
public IndelCall(StringTokenizer st) {
chr = st.nextToken();
pos = st.nextToken();
bases = st.nextToken();
type = st.nextToken();
if ( st.hasMoreTokens() )
id = st.nextToken();
count = 1;
}
}
public Integer reduceInit() { return 0; }
public void initialize() {
// set up the vcf writer
Set<String> samples = new HashSet<String>();
samples.add(sample);
writer.writeHeader(new VCFHeader(new HashSet<VCFHeaderLine>(), samples));
// read in the raw calls file
try {
AsciiLineReader lineReader = new AsciiLineReader(new FileInputStream(CG_FILE));
String line = lineReader.readLine();
while ( line != null ) {
StringTokenizer st = new StringTokenizer(line);
IndelCall call = new IndelCall(st);
String key = call.chr + ":" + call.pos;
if ( calls.containsKey(key) )
calls.get(key).count++;
else
calls.put(key, call);
line = lineReader.readLine();
}
}
catch (IOException e ) {
throw new ReviewedStingException(e.getMessage());
}
}
/**
*
* @param tracker the meta-data tracker
* @param ref the reference base
* @param context the context for the given locus
* @return 1 if the locus was successfully processed, 0 if otherwise
*/
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker == null )
return 0;
String pos = ref.getLocus().getContig() + ":" + ref.getLocus().getStart();
if ( !calls.containsKey(pos) ) {
System.out.println("We don't have any calls for position " + pos + " but somehow triggered here");
return 0;
}
IndelCall call = calls.get(pos);
Set<Allele> alleles = new HashSet<Allele>();
Map<String, Genotype> genotypes = new HashMap<String, Genotype>();
Allele refAllele, altAllele;
if ( call.type.equals("del") ) {
refAllele = Allele.create(call.bases, true);
altAllele = Allele.create(Allele.NULL_ALLELE_STRING, false);
} else if ( call.type.equals("ins") ) {
refAllele = Allele.create(Allele.NULL_ALLELE_STRING, true);
altAllele = Allele.create(call.bases, false);
} else {
System.out.println("Weird type seen for position " + pos + " -> " + call.type);
return 0;
}
alleles.add(refAllele);
alleles.add(altAllele);
long end = ref.getLocus().getStart() + (call.type.equals("del") ? call.bases.length() : 0);
List<Allele> myAlleles = new ArrayList<Allele>();
myAlleles.add(altAllele);
if ( call.count == 1 )
myAlleles.add(refAllele);
else
myAlleles.add(altAllele);
genotypes.put(sample, new Genotype(sample, myAlleles, -1));
Map<String, Object> attrs = new HashMap<String, Object>();
if ( call.id != null ) {
String rsID = call.id.substring(call.id.lastIndexOf(":")+1);
attrs.put(VariantContext.ID_KEY, rsID);
}
VariantContext vc = new VariantContext("CG",
ref.getLocus().getContig(),
ref.getLocus().getStart(),
end,
alleles,
genotypes,
-1,
null,
attrs);
writer.add(vc, ref.getBase());
return 1;
}
/**
* Increment the number of rods processed.
*
* @param value result of the map.
* @param sum accumulator for the reduce.
* @return the new number of rods processed.
*/
public Integer reduce(Integer value, Integer sum) {
return sum + value;
}
public void onTraversalDone(Integer result) {}
}

2
java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java → java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.walkers;
package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broadinstitute.sting.WalkerTest;
import org.testng.annotations.Test;