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

UG now downsamples to 250x by default 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4146 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-08-27 16:53:15 +00:00
parent 431392330e
commit 9584cbc05e
2 changed files with 3 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -31,6 +31,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
import org.broadinstitute.sting.gatk.DownsampleType;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.utils.vcf.VCFUtils; import org.broadinstitute.sting.utils.vcf.VCFUtils;
@ -45,6 +46,7 @@ import java.io.PrintStream;
*/ */
@Reference(window=@Window(start=-20,stop=20)) @Reference(window=@Window(start=-20,stop=20))
@By(DataSource.REFERENCE) @By(DataSource.REFERENCE)
@Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250)
public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGenotyper.UGStatistics> implements TreeReducible<UnifiedGenotyper.UGStatistics> { public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGenotyper.UGStatistics> implements TreeReducible<UnifiedGenotyper.UGStatistics> {
@ArgumentCollection private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection(); @ArgumentCollection private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -199,7 +199,7 @@ public class UnifiedGenotyperEngine {
call.setRefBase(ref); call.setRefBase(ref);
// if the site was downsampled, record that fact // if the site was downsampled, record that fact
if ( false ) { //rawContext.hasPileupBeenDownsampled() ) { if ( rawContext.hasPileupBeenDownsampled() ) {
Map<String, Object> attrs = new HashMap<String, Object>(call.vc.getAttributes()); Map<String, Object> attrs = new HashMap<String, Object>(call.vc.getAttributes());
attrs.put(VCFConstants.DOWNSAMPLED_KEY, true); attrs.put(VCFConstants.DOWNSAMPLED_KEY, true);
VariantContextUtils.modifyAttributes(call.vc, attrs); VariantContextUtils.modifyAttributes(call.vc, attrs);