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Added filter for bad cigars (based on consecutive indels) - and cleaned up bad mates filter. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3017 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-03-17 13:53:42 +00:00
parent 2cc040aa1c
commit af5fd99444
2 changed files with 56 additions and 6 deletions
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54
java/src/org/broadinstitute/sting/gatk/filters/BadCigarReadFilter.java 100755
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@ -0,0 +1,54 @@
/*
* Copyright (c) 2009 The Broad Institute
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.*;
/**
* Filter out reads with wonky cigar strings.
*
* @author ebanks
* @version 0.1
*/
public class BadCigarReadFilter implements SamRecordFilter {
public boolean filterOut(final SAMRecord rec) {
Cigar c = rec.getCigar();
boolean lastElementWasIndel = false;
for ( CigarElement ce : c.getCigarElements() ) {
if ( ce.getOperator() == CigarOperator.D || ce.getOperator() == CigarOperator.I ) {
if ( lastElementWasIndel )
return true;
lastElementWasIndel = true;
} else {
lastElementWasIndel = false;
}
}
return false;
}
}

8
java/src/org/broadinstitute/sting/gatk/filters/BadMateReadFilter.java
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@ -26,7 +26,6 @@ package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter; import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.cmdLine.Argument;
/** /**
* Filter out reads with low mapping qualities. * Filter out reads with low mapping qualities.
@ -37,10 +36,7 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
public class BadMateReadFilter implements SamRecordFilter { public class BadMateReadFilter implements SamRecordFilter {
@Argument(fullName = "use_reads_with_bad_mates", shortName = "bad_mates", doc = "Use reads whose mates are mapped excessively far away for calling", required = false) public boolean filterOut(final SAMRecord rec) {
public boolean USE_BADLY_MATED_READS = false; return (rec.getReadPairedFlag() && !rec.getMateUnmappedFlag() && rec.getMateReferenceIndex() != rec.getReferenceIndex());
public boolean filterOut(SAMRecord rec) {
return (!USE_BADLY_MATED_READS && rec.getReadPairedFlag() && !rec.getMateUnmappedFlag() && rec.getMateReferenceIndex() != rec.getReferenceIndex());
} }
} }