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Renaming for consistency 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3049 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-03-19 18:45:01 +00:00
parent 4c4d048f14
commit 4d4db7fe63
4 changed files with 9 additions and 11 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
View File

@ -13,7 +13,7 @@ public class ClusteredSnps {
throw new IllegalArgumentException("Window and threshold values need to be positive values");
}
public boolean filter(VariantContextWindow contextWindow) {
public boolean filter(FiltrationContextWindow contextWindow) {
FiltrationContext[] variants = contextWindow.getWindow(snpThreshold-1, snpThreshold-1);
for (int i = 0; i < snpThreshold; i++) {
@ -28,4 +28,4 @@ public class ClusteredSnps {
}
return false;
}
}
}

6
java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantContextWindow.java → java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
View File

@ -36,7 +36,7 @@ import java.util.*;
* @version 0.1
*/
public class VariantContextWindow {
public class FiltrationContextWindow {
/**
* The variants.
@ -48,7 +48,7 @@ public class VariantContextWindow {
* Contructor for a variant context.
* @param firstVariants the first set of variants, comprising the right half of the window
*/
public VariantContextWindow(List<FiltrationContext> firstVariants) {
public FiltrationContextWindow(List<FiltrationContext> firstVariants) {
int windowSize = (firstVariants == null ? 1 : 2 * firstVariants.size() + 1);
currentContext = (firstVariants == null ? 0 : firstVariants.size());
window.addAll(firstVariants);
@ -99,4 +99,4 @@ public class VariantContextWindow {
window.removeFirst();
window.addLast(context);
}
}
}

6
java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
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@ -55,7 +55,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
}
// the structures necessary to initialize and maintain a windowed context
private VariantContextWindow variantContextWindow;
private FiltrationContextWindow variantContextWindow;
private static final int windowSize = 10; // 10 variants on either end of the current one
private ArrayList<FiltrationContext> windowInitializer = new ArrayList<FiltrationContext>();
@ -119,7 +119,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
if ( windowInitializer != null ) {
windowInitializer.add(varContext);
if ( windowInitializer.size() == windowSize ) {
variantContextWindow = new VariantContextWindow(windowInitializer);
variantContextWindow = new FiltrationContextWindow(windowInitializer);
windowInitializer = null;
}
} else {
@ -194,7 +194,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
if ( windowInitializer != null ) {
while ( windowInitializer.size() < windowSize )
windowInitializer.add(null);
variantContextWindow = new VariantContextWindow(windowInitializer);
variantContextWindow = new FiltrationContextWindow(windowInitializer);
}
for (int i=0; i < windowSize; i++) {
variantContextWindow.moveWindow(null);

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSelectWalker.java
View File

@ -4,8 +4,6 @@ import org.broadinstitute.sting.gatk.contexts.*;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.filters.ClusteredSnps;
import org.broadinstitute.sting.gatk.walkers.filters.VariantContextWindow;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.genotype.vcf.*;
@ -134,4 +132,4 @@ public class VCFSelectWalker extends RodWalker<Integer, Integer> {
if ( writer != null )
writer.close();
}
}
}