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Use new optimized ReadBackedPileup 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2184 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-11-30 18:17:18 +00:00
parent d8146ab23d
commit e9a8156cfb
2 changed files with 9 additions and 17 deletions
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8
java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
View File

@ -12,12 +12,8 @@ import java.util.List;
public class SpanningDeletions extends StandardVariantAnnotation {
public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
int deletions = 0;
for (Integer offset : pileup.getOffsets() ) {
if ( offset == -1 )
deletions++;
}
return new Pair<String, String>("SpanningDeletionFraction", String.format("%.2f", (double)deletions/(double)pileup.getReads().size()));
int deletions = pileup.getNumberOfDeletions();
return new Pair<String, String>("SpanningDeletionFraction", String.format("%.2f", (double)deletions/(double)pileup.size()));
}
public boolean useZeroQualityReads() { return false; }

18
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
View File

@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.pileup.*;
import org.broadinstitute.sting.utils.genotype.*;
import org.broadinstitute.sting.utils.genotype.Variation.VARIANT_TYPE;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -10,8 +11,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import java.util.*;
import java.io.PrintWriter;
import net.sf.samtools.SAMRecord;
public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalculationModel {
// because the null allele frequencies are constant for a given N,
@ -77,19 +76,16 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
int[] qualCounts = new int[4];
// calculate the sum of quality scores for each base
List<SAMRecord> reads = context.getReads();
List<Integer> offsets = context.getOffsets();
for (int i = 0; i < reads.size(); i++) {
int offset = offsets.get(i);
ReadBackedPileup pileup = context.getPileup();
for ( PileupElement p : pileup ) {
byte base = p.getBase();
// ignore deletions
if ( offset == -1 )
if ( base == PileupElement.DELETION_BASE )
continue;
SAMRecord read = reads.get(i);
char base = (char)read.getReadBases()[offset];
int index = BaseUtils.simpleBaseToBaseIndex(base);
int index = BaseUtils.simpleBaseToBaseIndex((char)base);
if ( index >= 0 )
qualCounts[index] += read.getBaseQualities()[offset];
qualCounts[index] += p.getQual();
}
// set the non-ref base with maximum quality score sum