zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

No longer uses VCFRecord. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3762 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-07-12 13:34:10 +00:00
parent e75b3e13bd
commit f130d29318
1 changed files with 17 additions and 25 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

42
java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java
View File

@ -25,7 +25,6 @@
package org.broadinstitute.sting.playground.gatk.walkers;
import org.broad.tribble.vcf.VCFRecord;
import org.broad.tribble.vcf.VCFConstants;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -33,26 +32,25 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFReader;
import java.io.PrintStream;
import java.util.*;
/**
* Produces an input file to Beagle imputation engine, listing genotype likelihoods for each sample in input VCF file
* @help.summary Produces an input file to Beagle imputation engine, listing genotype likelihoods for each sample in input VCF file
* Produces an input file to Beagle imputation engine, listing genotype likelihoods for each sample in input variant file
*/
@Requires(value={},referenceMetaData=@RMD(name="vcf",type= VCFRecord.class))
@Requires(value={},referenceMetaData=@RMD(name=ProduceBeagleInputWalker.ROD_NAME, type=ReferenceOrderedDatum.class))
public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
public static final String ROD_NAME = "variant";
@Argument(fullName = "beagle_file", shortName = "beagle", doc = "File to print BEAGLE-specific data for use with imputation", required = true)
public PrintStream beagleWriter = null;
@Argument(fullName = "genotypes_file", shortName = "genotypes", doc = "File to print reference genotypes for error analysis", required = false)
@ -60,24 +58,13 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
@Argument(fullName = "inserted_nocall_rate", shortName = "nc_rate", doc = "Rate (0-1) at which genotype no-calls will be randomly inserted, for testing", required = false)
public double insertedNoCallRate = 0;
final TreeSet<String> samples = new TreeSet<String>();
Random generator;
public void initialize() {
final List<ReferenceOrderedDataSource> dataSources = this.getToolkit().getRodDataSources();
for ( final ReferenceOrderedDataSource source : dataSources ) {
final RMDTrack rod = source.getReferenceOrderedData();
if ( rod.getRecordType().equals(VCFRecord.class) ) {
final VCFReader reader = new VCFReader(rod.getFile());
final Set<String> vcfSamples = reader.getHeader().getGenotypeSamples();
samples.addAll(vcfSamples);
reader.close();
}
}
private TreeSet<String> samples = null;
private Random generator;
private void initialize(Set<String> sampleNames) {
generator = new Random();
beagleWriter.print("marker alleleA alleleB");
samples = new TreeSet<String>(sampleNames);
for ( String sample : samples )
beagleWriter.print(String.format(" %s %s %s", sample, sample, sample));
@ -85,21 +72,26 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
if (beagleGenotypesWriter != null)
beagleGenotypesWriter.println("dummy header");
}
public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
if( tracker != null ) {
GenomeLoc loc = context.getLocation();
VariantContext vc_eval;
vc_eval = tracker.getVariantContext(ref,"vcf", null, loc, false);
vc_eval = tracker.getVariantContext(ref, ROD_NAME, null, loc, false);
if ( vc_eval == null || vc_eval.isFiltered() )
return 0;
if ( samples == null ) {
initialize(vc_eval.getSampleNames());
}
// output marker ID to Beagle input file
beagleWriter.print(String.format("%s ",vc_eval.getLocation().toString()));
beagleWriter.print(String.format("%s ", vc_eval.getLocation().toString()));
if (beagleGenotypesWriter != null)
beagleGenotypesWriter.print(String.format("%s ",vc_eval.getLocation().toString()));
beagleGenotypesWriter.print(String.format("%s ", vc_eval.getLocation().toString()));
for (Allele allele: vc_eval.getAlleles()) {
// TODO -- check whether this is really needed by Beagle