ignore unmapped reads in all the indel walkers (since they're giving me overhead issues)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1224 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -9,6 +9,7 @@ import org.broadinstitute.sting.gatk.refdata.rodRefSeq;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.ReadFilters;
 import org.broadinstitute.sting.gatk.filters.Platform454Filter;
+import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
 import org.broadinstitute.sting.playground.utils.CircularArray;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
@@ -25,7 +26,7 @@ import java.util.List;
 import java.util.Set;
 
 
-@ReadFilters(Platform454Filter.class)
+@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class})
 public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
 	@Argument(fullName="bed", shortName="bed", doc="BED output file name", required=true)
 	java.io.File bed_file;

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

@@ -2,6 +2,9 @@ package org.broadinstitute.sting.playground.gatk.walkers.indels;
 
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
+import org.broadinstitute.sting.gatk.walkers.ReadFilters;
+import org.broadinstitute.sting.gatk.filters.Platform454Filter;
+import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.utils.*;
 import net.sf.samtools.SAMRecord;
@@ -15,6 +18,7 @@ import java.util.List;
 // although this can easily be changed if necessary.
 
 @WalkerName("IndelIntervals")
+@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class})
 public class IndelIntervalWalker extends ReadWalker<IndelIntervalWalker.Interval, IndelIntervalWalker.Interval> {
     @Argument(fullName="allow454Reads", shortName="454", doc="process 454 reads", required=false)
     boolean allow454 = false;

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

@@ -7,6 +7,7 @@ import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.gatk.walkers.ReadFilters;
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.filters.Platform454Filter;
+import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.playground.indels.*;
 
@@ -17,7 +18,7 @@ import java.io.File;
 import java.io.FileWriter;
  
 @WalkerName("IntervalCleaner")
-@ReadFilters(Platform454Filter.class)
+@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class})
 public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer> {
     @Argument(fullName="allow454Reads", shortName="454", doc="process 454 reads", required=false)
     boolean allow454 = false;

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

@@ -26,10 +26,9 @@ package org.broadinstitute.sting.playground.gatk.walkers.indels;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.filters.Platform454Filter;
-import org.broadinstitute.sting.gatk.walkers.WalkerName;
+import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
-import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
@@ -39,6 +38,7 @@ import java.util.*;
  */
 @WalkerName("IntervalMerger")
 @Requires({DataSource.READS})
+@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class})
 public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {
 
     @Argument(fullName="intervalsToMerge", shortName="intervals", doc="Intervals to merge", required=true)

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

@@ -5,13 +5,17 @@ import net.sf.samtools.*;
 import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.filters.Platform454Filter;
+import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
+import org.broadinstitute.sting.gatk.walkers.ReadFilters;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 import java.util.*;
 
 @WalkerName("MismatchIntervals")
+@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class})
 public class MismatchIntervalWalker extends LocusWalker<Pair<GenomeLoc, Boolean>, Pair<LinkedList<Boolean>, GenomeLoc>> {
     @Argument(fullName="windowSize", shortName="window", doc="window size for calculating entropy", required=false)
     int windowSize = 10;