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Moved some more walkers to oneoffprojects and killed an old indel-related walker that isn't being used. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2228 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-02 20:28:07 +00:00
parent dec0a781c2
commit a09fee2b5e
5 changed files with 4 additions and 75 deletions
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2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/MismatchCounterWalker.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers;
package org.broadinstitute.sting.oneoffprojects.walkers;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/MismatchHistoWalker.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers;
package org.broadinstitute.sting.oneoffprojects.walkers;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java → java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadErrorRateWalker.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers;
package org.broadinstitute.sting.oneoffprojects.walkers;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.cmdLine.Argument;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/ReplaceQuals.java → java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReplaceQuals.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers;
package org.broadinstitute.sting.oneoffprojects.walkers;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.cmdLine.Argument;

71
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/CoverageGapIntervalWalker.java
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@ -1,71 +0,0 @@
package org.broadinstitute.sting.playground.gatk.walkers.indels;
import net.sf.samtools.*;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import java.util.*;
@WalkerName("CoverageGapIntervals")
public class CoverageGapIntervalWalker extends LocusWalker<Pair<GenomeLoc, Integer>, GenomeLoc> {
private final int minReadsAtInterval = 10;
public void initialize() {}
public boolean filter(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
int goodReads = 0;
List<SAMRecord> reads = context.getReads();
for (int i = 0; i < reads.size(); i++ ) {
if ( reads.get(i).getMappingQuality() > 0 )
goodReads++;
}
return goodReads >= minReadsAtInterval;
}
public Pair<GenomeLoc, Integer> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
// find the probability that this locus has a statistically significant gap in coverage
List<SAMRecord> reads = context.getReads();
List<Integer> offsets = context.getOffsets();
int totalXi = 0;
for (int i = 0; i < reads.size(); i++ ) {
SAMRecord read = reads.get(i);
if ( read.getMappingQuality() == 0 )
continue;
int halfLength = read.getReadString().length() >> 1;
int distanceFromMiddle = Math.abs(offsets.get(i) - halfLength);
int quarterLength = halfLength >> 1;
// Xi is < 0 if you are closer to the middle than the quartile
// and is > 0 if further to the middle than quartile
// We expect the total sum of Xi over an interval to be ~0
int Xi = distanceFromMiddle - quarterLength;
totalXi += Xi;
}
return new Pair<GenomeLoc, Integer>(context.getLocation(), totalXi);
}
public void onTraversalDone() {}
public GenomeLoc reduceInit() {
return null;
}
public GenomeLoc reduce(Pair<GenomeLoc, Integer> value, GenomeLoc sum) {
if ( value.second > 1000 ) {
if ( sum != null )
sum = GenomeLocParser.setStop(sum,value.first.getStop());
else
sum = value.first;
} else if ( sum != null ) {
out.println(sum);
sum = null;
}
return sum;
}
}