79 lines
2.5 KiB
Java
79 lines
2.5 KiB
Java
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package org.broadinstitute.sting.oneoffprojects.walkers;
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import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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import org.broadinstitute.sting.alignment.bwa.BWAAligner;
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import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
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import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
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import org.broadinstitute.sting.alignment.Alignment;
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import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
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import org.broadinstitute.sting.utils.StingException;
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import net.sf.samtools.SAMRecord;
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import net.sf.samtools.SAMSequenceRecord;
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import net.sf.picard.reference.ReferenceSequence;
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import java.io.IOException;
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/**
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* A walker to experiment with fishing for reads in the GATK. Has very limited utility in its current state.
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*
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* @author mhanna
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* @version 0.1
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*/
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public class TestReadFishingWalker extends ReadWalker<Integer,Long> {
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/**
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* An aligner for the small custom reference.
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*/
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private BWAAligner aligner;
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@Override
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public void initialize() {
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ReferenceSequence initialBases;
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try {
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IndexedFastaSequenceFile reader = new IndexedFastaSequenceFile(getToolkit().getArguments().referenceFile);
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SAMSequenceRecord firstSequence = reader.getSequenceDictionary().getSequences().get(0);
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initialBases = reader.getSubsequenceAt(firstSequence.getSequenceName(),1,100);
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}
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catch(IOException ex) {
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throw new StingException("Unable to load initial bases from reference sequence");
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}
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aligner = new BWACAligner(initialBases.getBases(),new BWAConfiguration());
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}
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@Override
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public Integer map(char[] ref, SAMRecord read) {
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Alignment bestAlignment = aligner.getBestAlignment(read.getReadBases());
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System.out.println("bestAlignment = " + bestAlignment);
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return 1;
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}
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/**
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* Provide an initial value for reduce computations.
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* @return Initial value of reduce.
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*/
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@Override
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public Long reduceInit() {
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return 0L;
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}
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/**
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* Reduces a single map with the accumulator provided as the ReduceType.
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* @param value result of the map.
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* @param accum accumulator for the reduce.
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* @return accumulator with result of the map taken into account.
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*/
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@Override
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public Long reduce(Integer value, Long accum) {
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return value + accum;
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}
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@Override
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public void onTraversalDone(Long result) {
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aligner.close();
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super.onTraversalDone(result);
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}
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}
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