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update walkers so that onTraversalDone works (it now takes an arg) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@235 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-03-31 15:05:33 +00:00
parent 3896cc8f17
commit 907c183242
5 changed files with 4 additions and 10 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/AlignedReadsHistoWalker.java
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@ -45,7 +45,7 @@ public class AlignedReadsHistoWalker extends ReadWalker<Integer, Integer> {
return value + sum; return value + sum;
} }
public void onTraversalDone() { public void onTraversalDone(Integer result) {
int curTotal = 0; int curTotal = 0;
for ( int i = 0; i < alignCounts.length; i++ ) { for ( int i = 0; i < alignCounts.length; i++ ) {
curTotal += alignCounts[i]; curTotal += alignCounts[i];

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyMetricsWalker.java
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@ -159,7 +159,7 @@ public class AlleleFrequencyMetricsWalker extends LocusWalker<AlleleFrequencyEst
out.println(); out.println();
} }
public void onTraversalDone() public void onTraversalDone(String result)
{ {
printMetrics(); printMetrics();
} }

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityDumpWalker.java
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@ -4,12 +4,6 @@ import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.LocusContext; import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.WalkerName; import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.utils.Utils;
import edu.mit.broad.picard.reference.ReferenceSequence;
import java.util.Iterator;
import java.util.List;
import static java.lang.reflect.Array.*;
@WalkerName("Base_Quality_Dump") @WalkerName("Base_Quality_Dump")
public class BaseQualityDumpWalker extends ReadWalker<Integer, Integer> { public class BaseQualityDumpWalker extends ReadWalker<Integer, Integer> {

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityHistoWalker.java
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@ -43,7 +43,7 @@ public class BaseQualityHistoWalker extends ReadWalker<Integer, Integer> {
return value + sum; return value + sum;
} }
public void onTraversalDone() { public void onTraversalDone(Integer result) {
int lastNonZero = -1; int lastNonZero = -1;
for ( int i = this.qualCounts.length-1; i >= 0; i-- ) { for ( int i = this.qualCounts.length-1; i >= 0; i-- ) {
if ( this.qualCounts[i] > 0 ) { if ( this.qualCounts[i] > 0 ) {

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java
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@ -70,7 +70,7 @@ public class MismatchHistoWalker extends ReadWalker<Integer, Integer> {
return value + sum; return value + sum;
} }
public void onTraversalDone() { public void onTraversalDone(Integer result) {
for ( int i = 0; i < mismatchCounts.length; i++ ) for ( int i = 0; i < mismatchCounts.length; i++ )
out.println((i+1) + "\t" + mismatchCounts[i]); out.println((i+1) + "\t" + mismatchCounts[i]);
} }