Renaming read filters with a superfluous 'Read' in their names. Kept the ones that made sense to have it (e.g. MalformedReadFilter).

public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckFilter.java

@@ -34,7 +34,7 @@ import net.sf.samtools.SAMRecord;
  * Filter out FailsVendorQualityCheck reads.
  */
 
-public class FailsVendorQualityCheckReadFilter extends ReadFilter {
+public class FailsVendorQualityCheckFilter extends ReadFilter {
     public boolean filterOut( final SAMRecord read ) {
         return read.getReadFailsVendorQualityCheckFlag();
     }

public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityFilter.java

@@ -35,7 +35,7 @@ import org.broadinstitute.sting.commandline.Argument;
  * @version 0.1
  */
 
-public class MappingQualityReadFilter extends ReadFilter {
+public class MappingQualityFilter extends ReadFilter {
 
     @Argument(fullName = "min_mapping_quality_score", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for calling", required = false)
     public int MIN_MAPPING_QUALTY_SCORE = 10;

public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableFilter.java

@@ -34,7 +34,7 @@ import org.broadinstitute.sting.utils.QualityUtils;
  * @version 0.1
  */
 
-public class MappingQualityUnavailableReadFilter extends ReadFilter {
+public class MappingQualityUnavailableFilter extends ReadFilter {
     public boolean filterOut(SAMRecord rec) {
         return (rec.getMappingQuality() == QualityUtils.MAPPING_QUALITY_UNAVAILABLE);
     }

public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityZeroFilter.java

@@ -33,7 +33,7 @@ import net.sf.samtools.SAMRecord;
  * @version 0.1
  */
 
-public class MappingQualityZeroReadFilter extends ReadFilter {
+public class MappingQualityZeroFilter extends ReadFilter {
     public boolean filterOut(SAMRecord rec) {
         return (rec.getMappingQuality() == 0);
     }

public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentFilter.java

@@ -34,7 +34,7 @@ import net.sf.samtools.SAMRecord;
  * Filter out duplicate reads.
  */
 
-public class NotPrimaryAlignmentReadFilter extends ReadFilter {
+public class NotPrimaryAlignmentFilter extends ReadFilter {
     public boolean filterOut( final SAMRecord read ) {
         return read.getNotPrimaryAlignmentFlag();
     }

public/java/src/org/broadinstitute/sting/gatk/walkers/DuplicateWalker.java

@@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.filters.NotPrimaryAlignmentReadFilter;
+import org.broadinstitute.sting.gatk.filters.NotPrimaryAlignmentFilter;
 import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
@@ -17,7 +17,7 @@ import java.util.Set;
  * To change this template use File | Settings | File Templates.
  */
 @Requires({DataSource.READS,DataSource.REFERENCE})
-@ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentReadFilter.class})
+@ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentFilter.class})
 public abstract class DuplicateWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
     // Do we actually want to operate on the context?
     public boolean filter(GenomeLoc loc, AlignmentContext context, Set<List<SAMRecord>> readSets ) {

public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java

@@ -3,8 +3,8 @@ package org.broadinstitute.sting.gatk.walkers;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.filters.DuplicateReadFilter;
-import org.broadinstitute.sting.gatk.filters.FailsVendorQualityCheckReadFilter;
+import org.broadinstitute.sting.gatk.filters.FailsVendorQualityCheckFilter;
-import org.broadinstitute.sting.gatk.filters.NotPrimaryAlignmentReadFilter;
+import org.broadinstitute.sting.gatk.filters.NotPrimaryAlignmentFilter;
 import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 
@@ -18,7 +18,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 @By(DataSource.READS)
 @Requires({DataSource.READS,DataSource.REFERENCE, DataSource.REFERENCE_BASES})
 @PartitionBy(PartitionType.INTERVAL)
-@ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentReadFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckReadFilter.class})
+@ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckFilter.class})
 public abstract class LocusWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
     // Do we actually want to operate on the context?
     public boolean filter(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java

@@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.filters.BadMateFilter;
-import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter;
+import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
@@ -111,7 +111,7 @@ import java.util.*;
  */
 
 @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_INPUT)
-@ReadFilters( {BadMateFilter.class, MappingQualityUnavailableReadFilter.class} )
+@ReadFilters( {BadMateFilter.class, MappingQualityUnavailableFilter.class} )
 @Reference(window=@Window(start=-200,stop=200))
 @By(DataSource.REFERENCE)
 @Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250)

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java

@@ -33,7 +33,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.filters.BadCigarFilter;
 import org.broadinstitute.sting.gatk.filters.BadMateFilter;
-import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
+import org.broadinstitute.sting.gatk.filters.MappingQualityZeroFilter;
 import org.broadinstitute.sting.gatk.filters.Platform454Filter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
@@ -98,7 +98,7 @@ import java.util.List;
  *
  * @author ebanks
  */
-@ReadFilters({Platform454Filter.class, MappingQualityZeroReadFilter.class, BadCigarFilter.class})
+@ReadFilters({Platform454Filter.class, MappingQualityZeroFilter.class, BadCigarFilter.class})
 @Reference(window=@Window(start=-1,stop=50))
 @Allows(value={DataSource.READS, DataSource.REFERENCE})
 @By(DataSource.REFERENCE)

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java

@@ -33,7 +33,7 @@ import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
 import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
-import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
+import org.broadinstitute.sting.gatk.filters.MappingQualityZeroFilter;
 import org.broadinstitute.sting.gatk.filters.Platform454Filter;
 import org.broadinstitute.sting.gatk.filters.PlatformUnitFilter;
 import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper;
@@ -78,7 +78,7 @@ import java.util.*;
  * if first bam has coverage at the site but no indication for an indel. In the --somatic mode, BED output contains
  * only somatic calls, while --verbose output contains all calls annotated with GERMLINE/SOMATIC keywords.
  */
-@ReadFilters({Platform454Filter.class, MappingQualityZeroReadFilter.class, PlatformUnitFilter.class})
+@ReadFilters({Platform454Filter.class, MappingQualityZeroFilter.class, PlatformUnitFilter.class})
 public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
 //    @Output
 //    PrintStream out;

public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java

@@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgume
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
-import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
+import org.broadinstitute.sting.gatk.filters.MappingQualityZeroFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.BaseUtils;
@@ -91,7 +91,7 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr
 @By(DataSource.READS)
 
 // Filter out all reads with zero mapping quality
-@ReadFilters({MappingQualityZeroReadFilter.class})
+@ReadFilters({MappingQualityZeroFilter.class})
 
 public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, PhasingStats> {
     private static final boolean DEBUG = false;

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java

@@ -29,8 +29,8 @@ import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter;
+import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableFilter;
-import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
+import org.broadinstitute.sting.gatk.filters.MappingQualityZeroFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.BaseUtils;
@@ -97,7 +97,7 @@ import java.util.Map;
 
 @BAQMode(ApplicationTime = BAQ.ApplicationTime.FORBIDDEN)
 @By( DataSource.READS ) // Only look at covered loci, not every loci of the reference file
-@ReadFilters( {MappingQualityZeroReadFilter.class, MappingQualityUnavailableReadFilter.class} ) // Filter out all reads with zero or unavailable mapping quality
+@ReadFilters( {MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class} ) // Filter out all reads with zero or unavailable mapping quality
 @Requires( {DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES} ) // This walker requires both -I input.bam and -R reference.fasta
 @PartitionBy(PartitionType.LOCUS)
 public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.CountedData, CountCovariatesWalker.CountedData> implements TreeReducible<CountCovariatesWalker.CountedData> {