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A java reimplementation of vcf2table in python; supports getting more useful information about genotypes (HET, e.g.) than was possible in python. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4130 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-08-26 17:50:33 +00:00
parent 1e193e4c20
commit f384d4a5d6
1 changed files with 150 additions and 0 deletions
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java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java 100755
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/*
* Copyright (c) 2010, 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.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.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.Reference;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import java.io.PrintStream;
import java.util.*;
/**
* Combines VCF records from different sources; supports both full merges and set unions.
* Merge: combines multiple records into a single one; if sample names overlap then they are uniquified.
* Union: assumes each rod represents the same set of samples (although this is not enforced); using the
* priority list (if provided), emits a single record instance at every position represented in the rods.
*/
//@Reference(window=@Window(start=-50,stop=50))
@Requires(value={})
public class VariantsToTable extends RodWalker<Integer, Integer> {
@Output(doc="File to which variants should be written",required=true)
protected PrintStream out;
@Argument(fullName="fields", shortName="F", doc="Fields to emit from the VCF, allows any VCF field, any info field, and some meta fields like nHets", required=true)
public String FIELDS;
@Argument(fullName="maxRecords", shortName="M", doc="Maximum number of records to emit, if provided", required=false)
public int MAX_RECORDS = -1;
int nRecords = 0;
private List<String> fieldsToTake;
public void initialize() {
fieldsToTake = Arrays.asList(FIELDS.toUpperCase().split(","));
out.println(Utils.join("\t", fieldsToTake));
}
private static abstract class Getter { public abstract String get(VariantContext vc); }
private static Map<String, Getter> getters = new HashMap<String, Getter>();
static {
// #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
getters.put("CHROM", new Getter() { public String get(VariantContext vc) { return vc.getChr(); } });
getters.put("POS", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getStart()); } });
getters.put("REF", new Getter() { public String get(VariantContext vc) { return vc.getReference().toString(); } });
getters.put("ALT", new Getter() {
public String get(VariantContext vc) {
StringBuilder x = new StringBuilder();
int n = vc.getAlternateAlleles().size();
for ( int i = 0; i < n; i++ ) {
if ( i != 0 ) x.append(",");
x.append(vc.getAlternateAllele(i).toString());
}
return x.toString();
}
});
getters.put("QUAL", new Getter() { public String get(VariantContext vc) { return Double.toString(vc.getPhredScaledQual()); } });
getters.put("FILTER", new Getter() { public String get(VariantContext vc) { return Utils.join(",", vc.getFilters()); } });
getters.put("HET", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHetCount()); } });
getters.put("HOM-REF", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomRefCount()); } });
getters.put("HOM-VAR", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomVarCount()); } });
getters.put("NO-CALL", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getNoCallCount()); } });
getters.put("VAR", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHetCount() + vc.getHomVarCount()); } });
getters.put("NSAMPLES", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getNSamples()); } });
getters.put("NCALLED", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getNSamples() - vc.getNoCallCount()); } });
}
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker == null ) // RodWalkers can make funky map calls
return 0;
if ( ++nRecords < MAX_RECORDS || MAX_RECORDS == -1 ) {
Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, context.getLocation());
for ( VariantContext vc : vcs) {
List<String> vals = new ArrayList<String>();
for ( String field : fieldsToTake ) {
String val = "UNK";
if ( getters.containsKey(field) ) {
val = getters.get(field).get(vc);
} else if ( vc.hasAttribute(field) ) {
val = vc.getAttributeAsString(field);
}
vals.add(val);
}
out.println(Utils.join("\t", vals));
}
return 1;
} else {
if ( nRecords >= MAX_RECORDS ) {
logger.warn("Calling sys exit to leave after " + nRecords + " records");
System.exit(0); // todo -- what's the recommend way to abort like this?
}
return 0;
}
}
public Integer reduceInit() {
return 0;
}
public Integer reduce(Integer counter, Integer sum) {
return counter + sum;
}
public void onTraversalDone(Integer sum) {}
}