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

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

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"); 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); FiltrationContext[] variants = contextWindow.getWindow(snpThreshold-1, snpThreshold-1);
for (int i = 0; i < snpThreshold; i++) { for (int i = 0; i < snpThreshold; i++) {
@ -28,4 +28,4 @@ public class ClusteredSnps {
} }
return false; 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 * @version 0.1
*/ */
public class VariantContextWindow { public class FiltrationContextWindow {
/** /**
* The variants. * The variants.
@ -48,7 +48,7 @@ public class VariantContextWindow {
* Contructor for a variant context. * Contructor for a variant context.
* @param firstVariants the first set of variants, comprising the right half of the window * @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); int windowSize = (firstVariants == null ? 1 : 2 * firstVariants.size() + 1);
currentContext = (firstVariants == null ? 0 : firstVariants.size()); currentContext = (firstVariants == null ? 0 : firstVariants.size());
window.addAll(firstVariants); window.addAll(firstVariants);
@ -99,4 +99,4 @@ public class VariantContextWindow {
window.removeFirst(); window.removeFirst();
window.addLast(context); window.addLast(context);
} }
} }

6
java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
View File

@ -55,7 +55,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
} }
// the structures necessary to initialize and maintain a windowed context // 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 static final int windowSize = 10; // 10 variants on either end of the current one
private ArrayList<FiltrationContext> windowInitializer = new ArrayList<FiltrationContext>(); private ArrayList<FiltrationContext> windowInitializer = new ArrayList<FiltrationContext>();
@ -119,7 +119,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
if ( windowInitializer != null ) { if ( windowInitializer != null ) {
windowInitializer.add(varContext); windowInitializer.add(varContext);
if ( windowInitializer.size() == windowSize ) { if ( windowInitializer.size() == windowSize ) {
variantContextWindow = new VariantContextWindow(windowInitializer); variantContextWindow = new FiltrationContextWindow(windowInitializer);
windowInitializer = null; windowInitializer = null;
} }
} else { } else {
@ -194,7 +194,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
if ( windowInitializer != null ) { if ( windowInitializer != null ) {
while ( windowInitializer.size() < windowSize ) while ( windowInitializer.size() < windowSize )
windowInitializer.add(null); windowInitializer.add(null);
variantContextWindow = new VariantContextWindow(windowInitializer); variantContextWindow = new FiltrationContextWindow(windowInitializer);
} }
for (int i=0; i < windowSize; i++) { for (int i=0; i < windowSize; i++) {
variantContextWindow.moveWindow(null); 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.*;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.gatk.walkers.*; 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.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.genotype.vcf.*; import org.broadinstitute.sting.utils.genotype.vcf.*;
@ -134,4 +132,4 @@ public class VCFSelectWalker extends RodWalker<Integer, Integer> {
if ( writer != null ) if ( writer != null )
writer.close(); writer.close();
} }
} }