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

Fixes: 

- Don't know how I got the wiggle header so utterly wrong. Fixed.
 - Q-values now have a static maximum of 2000 so IGV averaging won't make everything look spikey and ugly.
 - Changing windows to size 100 for (hopefully) better resolution.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5406 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2011-03-08 17:16:21 +00:00
parent 1b310401fe
commit 31a2575c7b
14 changed files with 34 additions and 29 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

11
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/AssociationTestRunner.java
View File

@ -22,9 +22,14 @@ import org.broadinstitute.sting.utils.collections.Pair;
* To change this template use File | Settings | File Templates.
*/
public class AssociationTestRunner {
final static int MAX_Q_VALUE = 2000;
// todo -- this was written when ACs could implement interfaces, now that they extend, there's no multiple inheritance
static Normal standardNormal = new Normal(0.0,1.0,null);
private static int pToQ(double p) {
return Math.min((int) Math.floor(QualityUtils.phredScaleErrorRate(p)),MAX_Q_VALUE);
}
public static String runTests(AssociationContext context) {
List<String> results = new ArrayList<String>();
if ( context instanceof TStatistic) {
@ -58,15 +63,15 @@ public class AssociationTestRunner {
*/
public static int getQValue(AssociationContext context) {
if ( context instanceof TStatistic ) {
return (int) Math.floor(QualityUtils.phredScaleErrorRate(testStudentT((TStatistic) context).second));
return pToQ(testStudentT((TStatistic) context).second);
}
if ( context instanceof ZStatistic ) {
return (int) Math.floor(QualityUtils.phredScaleErrorRate(testZ((ZStatistic) context).second));
return pToQ(testZ((ZStatistic) context).second);
}
if ( context instanceof UStatistic ) {
return (int) Math.floor(QualityUtils.phredScaleErrorRate(mannWhitneyUTest((UStatistic) context).second));
return pToQ(mannWhitneyUTest((UStatistic) context).second);
}
return -1;

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/RegionalAssociationWalker.java
View File

@ -135,7 +135,7 @@ public class RegionalAssociationWalker extends LocusWalker<MapHolder, RegionalAs
public void writeWiggleHeaders(Set<AssociationContext> cons) {
for ( AssociationContext con : cons ) {
GenomeLoc first = getToolkit().getIntervals().iterator().next();
String header = String.format("fixedStep\tchrom=%s,start=%d,step=%d,span=%d",first.getContig(),first.getStart(),con.slideByValue(),con.getWindowSize());
String header = String.format("fixedStep chrom=%s start=%d step=%d span=%d",first.getContig(),first.getStart(),con.slideByValue(),con.getWindowSize());
out.get(con.getClass()).printf("%s%n",header);
}
}

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/BaseQualityScore.java
View File

@ -26,7 +26,7 @@ public class BaseQualityScore extends TStatistic {
return (Collection) baseQuals;
}
public int getWindowSize() { return 200; }
public int slideByValue() { return 25; }
public int getWindowSize() { return 100; }
public int slideByValue() { return 10; }
public boolean usePreviouslySeenReads() { return true; }
}

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/InsertSizeDistribution.java
View File

@ -13,8 +13,8 @@ import java.util.List;
* @author chartl
*/
public class InsertSizeDistribution extends TStatistic {
public int getWindowSize() { return 200; }
public int slideByValue() { return 25; }
public int getWindowSize() { return 100; }
public int slideByValue() { return 10; }
public boolean usePreviouslySeenReads() { return false; }
public Collection<Number> map(ReadBackedPileup pileup) {

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/MappingQuality0.java
View File

@ -26,8 +26,8 @@ public class MappingQuality0 extends ZStatistic {
return new Pair<Number,Number>(mq0,total);
}
public int getWindowSize() { return 200; }
public int slideByValue() { return 25; }
public int getWindowSize() { return 100; }
public int slideByValue() { return 10; }
public boolean usePreviouslySeenReads() { return false; }
}

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/MateMappingQuality.java
View File

@ -27,7 +27,7 @@ public class MateMappingQuality extends UStatistic {
return (Collection) mateMapQ;
}
public int getWindowSize() { return 200; }
public int slideByValue() { return 25; }
public int getWindowSize() { return 100; }
public int slideByValue() { return 10; }
public boolean usePreviouslySeenReads() { return false; }
}

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/MateOtherContig.java
View File

@ -14,8 +14,8 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
*/
public class MateOtherContig extends ZStatistic {
public int getWindowSize() { return 200; }
public int slideByValue() { return 25; }
public int getWindowSize() { return 100; }
public int slideByValue() { return 10; }
public boolean usePreviouslySeenReads() { return false; }
public Pair<Number,Number> map(ReadBackedPileup pileup) {

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/MateSameStrand.java
View File

@ -29,7 +29,7 @@ public class MateSameStrand extends ZStatistic {
return new Pair<Number,Number>(mateSameStrand,numPairs);
}
public int getWindowSize() { return 200; }
public int slideByValue() { return 25; }
public int getWindowSize() { return 100; }
public int slideByValue() { return 10; }
public boolean usePreviouslySeenReads() { return false; }
}

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/MateUnmapped.java
View File

@ -29,7 +29,7 @@ public class MateUnmapped extends ZStatistic {
return new Pair<Number,Number>(numPairUnmapped,numMatedReads);
}
public int getWindowSize() { return 200; }
public int slideByValue() { return 25; }
public int getWindowSize() { return 100; }
public int slideByValue() { return 10; }
public boolean usePreviouslySeenReads() { return false; }
}

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/ProperPairs.java
View File

@ -27,7 +27,7 @@ public class ProperPairs extends ZStatistic {
return new Pair<Number,Number>(numPropPair,numReads);
}
public int getWindowSize() { return 200; }
public int slideByValue() { return 25; }
public int getWindowSize() { return 100; }
public int slideByValue() { return 10; }
public boolean usePreviouslySeenReads() { return false; }
}

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/ReadClipping.java
View File

@ -33,7 +33,7 @@ public class ReadClipping extends TStatistic {
return (Collection) clipping;
}
public int getWindowSize() { return 200; }
public int slideByValue() { return 25; }
public int getWindowSize() { return 100; }
public int slideByValue() { return 10; }
public boolean usePreviouslySeenReads() { return false; }
}

6
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/ReadIndels.java
View File

@ -17,7 +17,7 @@ import java.util.Collection;
* Time: 1:54 PM
* To change this template use File | Settings | File Templates.
*/
public class ReadIndels extends TStatistic {
public class ReadIndels extends UStatistic {
public Collection<Number> map(ReadBackedPileup rbp) {
ArrayList<Integer> indelElements = new ArrayList<Integer>(rbp.size());
@ -33,7 +33,7 @@ public class ReadIndels extends TStatistic {
return (Collection) indelElements;
}
public int getWindowSize() { return 200; }
public int slideByValue() { return 25; }
public int getWindowSize() { return 100; }
public int slideByValue() { return 10; }
public boolean usePreviouslySeenReads() { return false; }
}

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/ReadMappingQuality.java
View File

@ -26,7 +26,7 @@ public class ReadMappingQuality extends TStatistic {
return (Collection) mapQuals;
}
public int getWindowSize() { return 200; }
public int slideByValue() { return 25; }
public int getWindowSize() { return 100; }
public int slideByValue() { return 10; }
public boolean usePreviouslySeenReads() { return false; }
}

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/SampleDepth.java
View File

@ -75,8 +75,8 @@ public class SampleDepth extends UStatistic {
// note: this is to satisfy the interface, and is never called due to override
public Collection<Number> map(ReadBackedPileup pileup) { return null; }
public int getWindowSize() { return 200; }
public int slideByValue() { return 25; }
public int getWindowSize() { return 100; }
public int slideByValue() { return 10; }
public boolean usePreviouslySeenReads() { return true; }