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

Some cleanup 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2382 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-16 21:41:06 +00:00
parent bb92e31118
commit bef1c50b3b
1 changed files with 4 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

9
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -38,7 +38,6 @@ import org.broadinstitute.sting.utils.genotype.*;
import org.broadinstitute.sting.utils.genotype.vcf.*; import org.broadinstitute.sting.utils.genotype.vcf.*;
import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMReadGroupRecord;
import net.sf.picard.filter.SamRecordFilter;
import java.io.File; import java.io.File;
import java.util.*; import java.util.*;
@ -184,10 +183,10 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
headerInfo.addAll(VCFGenotypeRecord.getSupportedHeaderStrings()); headerInfo.addAll(VCFGenotypeRecord.getSupportedHeaderStrings());
// all of the arguments from the argument collection // all of the arguments from the argument collection
Set<Object> x = new HashSet<Object>(); Set<Object> args = new HashSet<Object>();
x.add(UAC); args.add(UAC);
x.addAll(getToolkit().getFilters()); args.addAll(getToolkit().getFilters());
Map<String,String> commandLineArgs = CommandLineUtils.getApproximateCommandLineArguments(x); Map<String,String> commandLineArgs = CommandLineUtils.getApproximateCommandLineArguments(args);
for ( Map.Entry<String, String> commandLineArg : commandLineArgs.entrySet() ) for ( Map.Entry<String, String> commandLineArg : commandLineArgs.entrySet() )
headerInfo.add(new VCFHeaderLine(String.format("UG_%s", commandLineArg.getKey()), commandLineArg.getValue())); headerInfo.add(new VCFHeaderLine(String.format("UG_%s", commandLineArg.getKey()), commandLineArg.getValue()));