diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MismatchCounterWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MismatchCounterWalker.java index ca83dbccf..aca16e812 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MismatchCounterWalker.java +++ b/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; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MismatchHistoWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MismatchHistoWalker.java index cd90169b3..7945d2ac5 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MismatchHistoWalker.java +++ b/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; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadErrorRateWalker.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java rename to java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadErrorRateWalker.java index 80ff49af9..2db84b5a9 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java +++ b/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; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReplaceQuals.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReplaceQuals.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/ReplaceQuals.java rename to java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReplaceQuals.java index d5c443ae3..e36e2a8e5 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReplaceQuals.java +++ b/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; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/CoverageGapIntervalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/CoverageGapIntervalWalker.java deleted file mode 100755 index 0c1b787da..000000000 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/CoverageGapIntervalWalker.java +++ /dev/null @@ -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, GenomeLoc> { - - private final int minReadsAtInterval = 10; - - public void initialize() {} - - public boolean filter(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - int goodReads = 0; - List reads = context.getReads(); - for (int i = 0; i < reads.size(); i++ ) { - if ( reads.get(i).getMappingQuality() > 0 ) - goodReads++; - } - return goodReads >= minReadsAtInterval; - } - - public Pair map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - // find the probability that this locus has a statistically significant gap in coverage - List reads = context.getReads(); - List 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(context.getLocation(), totalXi); - } - - public void onTraversalDone() {} - - public GenomeLoc reduceInit() { - return null; - } - - public GenomeLoc reduce(Pair 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; - } -} \ No newline at end of file