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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
This commit is contained in:
ebanks 2009-07-13 16:51:11 +00:00
parent 5c321f9630
commit 52659d02d4
5 changed files with 16 additions and 6 deletions
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3
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
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@ -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;

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelIntervalWalker.java
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@ -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;

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
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@ -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;

8
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalMergerWalker.java
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@ -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.walkers.WalkerName;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.filters.Platform454Filter;
import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
import org.broadinstitute.sting.gatk.walkers.*;
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)

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java
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@ -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;