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Adding in some read filters, updating MathUtils. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6042 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
droazen 2011-06-22 22:54:15 +00:00
parent e0d203434f
commit 84dd72e6cb
2 changed files with 39 additions and 0 deletions
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18
java/src/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java 100755
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package org.broadinstitute.sting.gatk.filters;
import net.sf.samtools.SAMRecord;
/**
* Created by IntelliJ IDEA.
* User: chartl
* Date: 5/18/11
* Time: 4:25 PM
* To change this template use File | Settings | File Templates.
*/
public class MateSameStrandFilter extends ReadFilter {
public boolean filterOut(SAMRecord read) {
return (! read.getReadPairedFlag() ) || read.getMateUnmappedFlag() || read.getDuplicateReadFlag() ||
read.getReadFailsVendorQualityCheckFlag() || read.getMateNegativeStrandFlag() != read.getReadNegativeStrandFlag();
}
}

21
java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java 100755
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package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Argument;
/**
* Created by IntelliJ IDEA.
* User: chartl
* Date: 5/2/11
* Time: 12:20 PM
* To change this template use File | Settings | File Templates.
*/
public class MaxInsertSizeFilter extends ReadFilter {
@Argument(fullName = "maxInsertSize", shortName = "maxInsert", doc="Discard reads with insert size greater than the specified value, defaults to 1000000", required=false)
private int maxInsertSize = 1000000;
public boolean filterOut(SAMRecord record) {
return (record.getReadPairedFlag() && (record.getInferredInsertSize() > maxInsertSize || record.getInferredInsertSize() < -1*maxInsertSize));
}
}