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Automatically filter out reads with consecutive indel operators in the CIGAR string 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4914 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-12-31 04:42:54 +00:00
parent 848977678d
commit d70483c50a
1 changed files with 3 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
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@ -28,13 +28,13 @@ package org.broadinstitute.sting.gatk.walkers.indels;
import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.filters.BadCigarFilter;
import org.broadinstitute.sting.gatk.filters.Platform454Filter; import org.broadinstitute.sting.gatk.filters.Platform454Filter;
import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter; import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
import org.broadinstitute.sting.gatk.filters.BadMateFilter; import org.broadinstitute.sting.gatk.filters.BadMateFilter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Output;
@ -48,9 +48,9 @@ import java.util.ArrayList;
import java.io.PrintStream; import java.io.PrintStream;
/** /**
* Emits intervals for the Local Indel Realigner to target for cleaning. Ignores 454 and MQ0 reads. * Emits intervals for the Local Indel Realigner to target for cleaning. Ignores 454 reads, MQ0 reads, and reads with consecutive indel operators in the CIGAR string.
*/ */
@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class}) @ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class, BadCigarFilter.class})
@Reference(window=@Window(start=-1,stop=50)) @Reference(window=@Window(start=-1,stop=50))
@Allows(value={DataSource.READS, DataSource.REFERENCE}) @Allows(value={DataSource.READS, DataSource.REFERENCE})
@By(DataSource.REFERENCE) @By(DataSource.REFERENCE)