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

added new required annotations 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@736 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kcibul 2009-05-17 12:24:06 +00:00
parent 28bf7ec8ad
commit bd53bc18f9
1 changed files with 8 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticMutationWalker.java
View File

@ -6,6 +6,8 @@ import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.refdata.HapMapAlleleFrequenciesROD;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.By;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.playground.utils.GenotypeLikelihoods;
import net.sf.samtools.SAMRecord;
@ -14,6 +16,7 @@ import java.util.List;
import java.util.HashMap;
import java.util.Map;
@By(DataSource.REFERENCE)
public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
protected static class QualitySums {
private int a = 0;
@ -73,6 +76,8 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
public static int MIN_MUTANT_SUM_PRETEST = 60;
public static int MIN_MUTANT_SUM = 100;
public static int MIN_QSCORE = 13;
public static double TUMOR_LOD = 6.3d;
// public static double TUMOR_LOD = 1.0d;
public static double NORMAL_LOD = 2.3d;
@ -138,11 +143,11 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
if (normalSampleName.equals(sample)) {
normalGL.add(ref, base, qual);
normalQualitySums.incrementSum(base, qual);
if (qual > MIN_QSCORE) normalQualitySums.incrementSum(base, qual);
normalBases.append(base);
} else if (tumorSampleName.equals(sample)) {
tumorGL.add(ref, base, qual);
tumorQualitySums.incrementSum(base, qual);
if (qual > MIN_QSCORE) tumorQualitySums.incrementSum(base, qual);
tumorBases.append(base);
int midDist = Math.abs((int)(read.getReadLength() / 2) - offset);
@ -204,6 +209,7 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
"__NScore:" + normalLod +
"__NRefSum: " + normalQualitySums.get(ref) +
"__NAltSum: " + normalQualitySums.get(altAllele) +
"__MIDP: " + midp.get(altAllele) +
(failedMidpointCheck?"__FAILED-MPCHECK":"")
);