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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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10
public/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCMappingQualityFilter.java
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@ -26,7 +26,9 @@
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);
} }