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Display the active MappingQualityFilter if mmq > 0 in the HaplotypeCaller

This commit is contained in:
Mark DePristo 2013-03-24 14:42:48 -04:00
parent ad04fdb233
commit 12475cc027
1 changed files with 33 additions and 23 deletions
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56
public/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCMappingQualityFilter.java
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@ -1,32 +1,34 @@
/* /*
* Copyright (c) 2012 The Broad Institute * Copyright (c) 2012 The Broad Institute
* *
* Permission is hereby granted, free of charge, to any person * Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation * obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without * files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use, * restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell * copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the * copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following * Software is furnished to do so, subject to the following
* conditions: * conditions:
* *
* The above copyright notice and this permission notice shall be * The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software. * included in all copies or substantial portions of the Software.
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE. * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/ */
package org.broadinstitute.sting.gatk.walkers.haplotypecaller; package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.filters.ReadFilter; import org.broadinstitute.sting.gatk.filters.ReadFilter;
/** /**
@ -35,9 +37,17 @@ import org.broadinstitute.sting.gatk.filters.ReadFilter;
* @author mdepristo * @author mdepristo
*/ */
public class HCMappingQualityFilter extends ReadFilter { public class HCMappingQualityFilter extends ReadFilter {
private final static Logger logger = Logger.getLogger(HCMappingQualityFilter.class);
@Argument(fullName = "min_mapping_quality_score", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for analysis with the HaplotypeCaller", required = false) @Argument(fullName = "min_mapping_quality_score", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for analysis with the HaplotypeCaller", required = false)
public int MIN_MAPPING_QUALTY_SCORE = 20; public int MIN_MAPPING_QUALTY_SCORE = 20;
@Override
public void initialize(GenomeAnalysisEngine engine) {
if ( MIN_MAPPING_QUALTY_SCORE > 0 )
logger.info("Filtering out reads with MAPQ < " + MIN_MAPPING_QUALTY_SCORE);
}
public boolean filterOut(SAMRecord rec) { public boolean filterOut(SAMRecord rec) {
return (rec.getMappingQuality() < MIN_MAPPING_QUALTY_SCORE); return (rec.getMappingQuality() < MIN_MAPPING_QUALTY_SCORE);
} }