63 lines
1.7 KiB
Java
63 lines
1.7 KiB
Java
package org.broadinstitute.sting.utils.sam;
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import net.sf.samtools.SAMFileHeader;
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import net.sf.samtools.SAMFileWriter;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import java.util.Iterator;
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import java.util.NoSuchElementException;
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/**
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* XXX
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*/
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public class SimplifyingSAMFileWriter implements SAMFileWriter {
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final SAMFileWriter dest;
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public SimplifyingSAMFileWriter(final SAMFileWriter finalDestination) {
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this.dest = finalDestination;
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}
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public void addAlignment( SAMRecord read ) {
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if ( keepRead(read) ) {
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dest.addAlignment(simplifyRead(read));
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}
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}
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/**
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* Retrieves the header to use when creating the new SAM file.
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* @return header to use when creating the new SAM file.
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*/
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public SAMFileHeader getFileHeader() {
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return dest.getFileHeader();
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}
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/**
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* @{inheritDoc}
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*/
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public void close() {
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dest.close();
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}
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public static final boolean keepRead(SAMRecord read) {
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return ! excludeRead(read);
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}
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public static final boolean excludeRead(SAMRecord read) {
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return read.getReadUnmappedFlag() || read.getReadFailsVendorQualityCheckFlag() || read.getDuplicateReadFlag() || read.getNotPrimaryAlignmentFlag();
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}
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public static final SAMRecord simplifyRead(SAMRecord read) {
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// the only attribute we keep is the RG
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Object rg = read.getAttribute("RG");
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read.clearAttributes();
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read.setAttribute("RG", rg);
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return read;
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}
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}
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