zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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

This commit is contained in:
Eric Banks 2011-08-18 22:01:33 -04:00
parent 09d099cada
commit 77fa2c1546
12 changed files with 21 additions and 21 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckReadFilter.java → public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckFilter.java
View File

@ -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();
}

2
public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java → public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityFilter.java
View File

@ -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;

2
public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java → public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableFilter.java
View File

@ -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);
}

2
public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityZeroReadFilter.java → public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityZeroFilter.java
View File

@ -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);
}

2
public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentReadFilter.java → public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentFilter.java
View File

@ -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();
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/DuplicateWalker.java
View File

@ -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 ) {

6
public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
View File

@ -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.NotPrimaryAlignmentReadFilter;
import org.broadinstitute.sting.gatk.filters.FailsVendorQualityCheckFilter;
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) {

4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -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)

4
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
View File

@ -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)

4
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
View File

@ -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;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
View File

@ -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;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
View File

@ -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.MappingQualityZeroReadFilter;
import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableFilter;
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> {