126 lines
4.4 KiB
Java
126 lines
4.4 KiB
Java
package org.broadinstitute.sting.alignment;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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import org.broadinstitute.sting.gatk.walkers.WalkerName;
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import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
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import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
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import org.broadinstitute.sting.alignment.bwa.BWTFiles;
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import net.sf.samtools.*;
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import net.sf.picard.reference.ReferenceSequenceFileFactory;
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/**
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* Align reads to the reference specified by BWTPrefix.
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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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@WalkerName("Align")
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public class AlignmentWalker extends ReadWalker<Integer,Integer> {
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@Argument(fullName="BWTPrefix",shortName="BWT",doc="Index files generated by bwa index -d bwtsw",required=false)
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String prefix = "/Users/mhanna/reference/Ecoli/Escherichia_coli_K12_MG1655.fasta";
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@Argument(fullName = "outputBam", shortName = "ob", doc = "Write output to this BAM filename instead of STDOUT", required = false)
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String outputBamFile = null;
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@Argument(fullName = "bam_compression", shortName = "compress", doc = "Compression level to use for writing BAM files", required = false)
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public Integer bamCompression = 5;
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/**
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* The actual aligner.
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*/
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private BWACAligner aligner = null;
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/**
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* Target for reads to output.
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*/
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private SAMFileWriter outputBam = null;
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/**
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* New header to use, if desired.
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*/
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private SAMFileHeader header = null;
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/** Must return true for reads that need to be processed. Reads, for which this method return false will
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* be skipped by the engine and never passed to the walker.
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*/
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@Override
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public boolean filter(char[] ref, SAMRecord read) {
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return true;
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}
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/**
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* Create an aligner object. The aligner object will load and hold the BWT until close() is called.
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*/
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@Override
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public void initialize() {
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BWTFiles bwtFiles = new BWTFiles(prefix);
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BWAConfiguration configuration = new BWAConfiguration();
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aligner = new BWACAligner(bwtFiles,configuration);
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// HACK: If the sequence dictionary in the existing header is null, stuff the contents of the current reference
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// into it, so that the sequence has something to which to back-align.
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SAMFileHeader originalHeader = getToolkit().getSAMFileHeader();
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if(originalHeader.getSequenceDictionary().isEmpty()) {
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header = originalHeader.clone();
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SAMSequenceDictionary referenceDictionary =
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ReferenceSequenceFileFactory.getReferenceSequenceFile(getToolkit().getArguments().referenceFile).getSequenceDictionary();
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header.setSequenceDictionary(referenceDictionary);
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}
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else
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header = originalHeader;
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if ( outputBamFile != null ) {
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// Stuff the header from the fasta into that of the sequence dictionary.
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outputBam = Utils.createSAMFileWriterWithCompression(header, false, outputBamFile, bamCompression);
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}
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}
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/**
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* Aligns a read to the given reference.
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* @param ref Reference over the read. Read will most likely be unmapped, so ref will be null.
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* @param read Read to align.
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* @return Number of alignments found for this read.
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*/
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@Override
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public Integer map(char[] ref, SAMRecord read) {
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SAMRecord alignedRead = aligner.align(read,header);
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if (outputBam != null) {
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outputBam.addAlignment(alignedRead);
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} else {
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out.println(alignedRead.format());
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}
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return 1;
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}
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/**
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* Initial value for reduce. In this case, alignments will be counted.
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* @return 0, indicating no alignments yet found.
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*/
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@Override
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public Integer reduceInit() { return 0; }
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/**
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* Calculates the number of alignments found.
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* @param value Number of alignments found by this map.
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* @param sum Number of alignments found before this map.
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* @return Number of alignments found up to and including this map.
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*/
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@Override
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public Integer reduce(Integer value, Integer sum) {
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return value + sum;
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}
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/**
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* Cleanup.
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* @param result Number of reads processed.
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*/
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@Override
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public void onTraversalDone(Integer 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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