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

java/src/org/broadinstitute/sting/oneoffprojects/walkers/MismatchCounterWalker.java

@@ -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;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/MismatchHistoWalker.java

@@ -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;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadErrorRateWalker.java

@@ -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;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReplaceQuals.java

@@ -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;

java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/CoverageGapIntervalWalker.java

@@ -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;
-    }
-}