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@ Hack to allow output from onTraversalDone() 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1908 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-10-25 15:19:04 +00:00
parent 75ad6bbef7
commit db9419df49
1 changed files with 16 additions and 2 deletions
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18
java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
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@ -12,6 +12,8 @@ import org.broadinstitute.sting.utils.genotype.GenotypeMetaData;
import java.util.*; import java.util.*;
import java.io.PrintStream; import java.io.PrintStream;
import java.io.PrintWriter; import java.io.PrintWriter;
import java.io.OutputStream;
import java.io.FileNotFoundException;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
@ -43,6 +45,8 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
int nPreviousReadBases = 0; int nPreviousReadBases = 0;
@Argument(fullName="useReadGroup", doc="Use the group number of the read as a condition of the table.", required = false) @Argument(fullName="useReadGroup", doc="Use the group number of the read as a condition of the table.", required = false)
boolean useReadGroup = false; boolean useReadGroup = false;
@Argument(fullName="outputFile", shortName="of", doc="Output to this file rather than standard out. Must be used with -nt.", required = false)
String outFilePath = null;
private UnifiedGenotyper ug; private UnifiedGenotyper ug;
// private ReferenceContextWindow refWindow; // private ReferenceContextWindow refWindow;
@ -116,9 +120,19 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
} }
public void onTraversalDone( Set<BaseTransitionTable> conditionalTables ) { public void onTraversalDone( Set<BaseTransitionTable> conditionalTables ) {
out.print(createHeaderFromConditions()); PrintStream output;
if ( outFilePath == null ) {
output = out;
} else {
try {
output = new PrintStream(outFilePath);
} catch ( FileNotFoundException e ) {
throw new StingException("File given as input to -of, "+outFilePath+" could not be opened.",e);
}
}
output.print(createHeaderFromConditions());
for ( BaseTransitionTable t : conditionalTables ) for ( BaseTransitionTable t : conditionalTables )
t.print(out); t.print(output);
} }
public void updatePreviousBases(List<Boolean> usage, boolean canUse, List<GenomeLoc> loci, GenomeLoc locus) { public void updatePreviousBases(List<Boolean> usage, boolean canUse, List<GenomeLoc> loci, GenomeLoc locus) {