69 lines
2.7 KiB
Java
Executable File
69 lines
2.7 KiB
Java
Executable File
package org.broadinstitute.sting.gatk.walkers;
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import org.broadinstitute.sting.gatk.filters.*;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.traversals.TraversalStatistics;
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import org.broadinstitute.sting.gatk.iterators.LocusIteratorByState;
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import org.broadinstitute.sting.gatk.iterators.LocusIteratorFilter;
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import net.sf.picard.filter.SamRecordFilter;
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import net.sf.samtools.SAMRecord;
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import java.util.List;
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import java.util.Arrays;
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import java.util.EnumSet;
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/**
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* Created by IntelliJ IDEA.
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* User: mdepristo
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* Date: Feb 22, 2009
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* Time: 2:52:28 PM
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* To change this template use File | Settings | File Templates.
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*/
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@By(DataSource.READS)
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@Requires({DataSource.READS,DataSource.REFERENCE, DataSource.REFERENCE_BASES})
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public abstract class LocusWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
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// Do we actually want to operate on the context?
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public boolean filter(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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return true; // We are keeping all the reads
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}
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// Map over the org.broadinstitute.sting.gatk.contexts.AlignmentContext
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public abstract MapType map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context);
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// --------------------------------------------------------------------------------------------------------------
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//
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// mandatory read filters
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//
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// --------------------------------------------------------------------------------------------------------------
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public List<SamRecordFilter> getMandatoryReadFilters() {
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// if ( false ) {
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// SamRecordFilter filter = new LocusStreamFilterFunc();
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// return Arrays.asList(filter);
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// } else {
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SamRecordFilter filter1 = new UnmappedReadFilter();
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SamRecordFilter filter2 = new NotPrimaryAlignmentReadFilter();
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SamRecordFilter filter3 = new DuplicateReadFilter();
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SamRecordFilter filter4 = new FailsVendorQualityCheckReadFilter();
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List<SamRecordFilter> x = super.getMandatoryReadFilters();
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x.addAll(Arrays.asList(filter4, filter3, filter2, filter1));
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// }
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return x;
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}
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/**
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* Returns the set of locus iterator discards that this walker wants the engine to discard automatically
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*
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* By default, locus walkers ignore adaptor bases but still see the both bases in the overlapping but non-adaptor
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* parts of the reads.
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* @return
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*/
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public List<LocusIteratorFilter> getDiscards() {
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LocusIteratorFilter filter = new InAdaptorFilter();
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return Arrays.asList(filter);
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}
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}
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