116 lines
5.5 KiB
Java
116 lines
5.5 KiB
Java
package org.broadinstitute.sting.alignment.bwa;
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import org.broadinstitute.sting.alignment.bwa.bwt.*;
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import org.broadinstitute.sting.alignment.Aligner;
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import org.broadinstitute.sting.alignment.Alignment;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.util.List;
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import net.sf.samtools.SAMRecord;
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import net.sf.samtools.SAMFileReader;
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/**
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* A test harness to ensure that the perfect aligner works.
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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 AlignerTestHarness {
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public static void main( String argv[] ) throws FileNotFoundException {
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if( argv.length != 6 ) {
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System.out.println("PerfectAlignerTestHarness <fasta> <bwt> <rbwt> <sa> <rsa> <bam>");
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System.exit(1);
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}
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File referenceFile = new File(argv[0]);
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File bwtFile = new File(argv[1]);
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File rbwtFile = new File(argv[2]);
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File suffixArrayFile = new File(argv[3]);
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File reverseSuffixArrayFile = new File(argv[4]);
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File bamFile = new File(argv[5]);
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align(referenceFile,bwtFile,rbwtFile,suffixArrayFile,reverseSuffixArrayFile,bamFile);
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}
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private static void align(File referenceFile, File bwtFile, File rbwtFile, File suffixArrayFile, File reverseSuffixArrayFile, File bamFile) throws FileNotFoundException {
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Aligner aligner = new BWAAligner(bwtFile,rbwtFile,suffixArrayFile,reverseSuffixArrayFile);
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int count = 0;
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SAMFileReader reader = new SAMFileReader(bamFile);
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reader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
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for(SAMRecord read: reader) {
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count++;
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//if( count > 25000 ) break;
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//if( count != 39 ) continue;
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//if( !read.getReadName().endsWith("1507:1636#0") )
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// continue;
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SAMRecord alignmentCleaned = null;
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try {
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alignmentCleaned = (SAMRecord)read.clone();
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}
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catch( CloneNotSupportedException ex ) {
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throw new StingException("SAMRecord clone not supported", ex);
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}
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if( alignmentCleaned.getReadNegativeStrandFlag() )
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alignmentCleaned.setReadBases(BaseUtils.simpleReverseComplement(alignmentCleaned.getReadBases()));
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alignmentCleaned.setReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
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alignmentCleaned.setAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
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alignmentCleaned.setMappingQuality(SAMRecord.NO_MAPPING_QUALITY);
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alignmentCleaned.setCigarString(SAMRecord.NO_ALIGNMENT_CIGAR);
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// Clear everything except flags pertaining to pairing and set 'unmapped' status to true.
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alignmentCleaned.setFlags(alignmentCleaned.getFlags() & 0x00A1 | 0x000C);
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List<Alignment> alignments = aligner.align(alignmentCleaned);
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if(alignments.size() == 0 )
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throw new StingException(String.format("Unable to align read %s to reference; count = %d",read.getReadName(),count));
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Alignment alignment = alignments.get(0);
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System.out.printf("%s: Aligned read to reference at position %d with %d mismatches, %d gap opens, and %d gap extensions.%n", read.getReadName(), alignment.getAlignmentStart(), alignment.getMismatches(), alignment.getGapOpens(), alignment.getGapExtensions());
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if( read.getReadNegativeStrandFlag() != alignment.isNegativeStrand() )
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throw new StingException("Read has been aligned in wrong direction");
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if( read.getAlignmentStart() != alignment.getAlignmentStart() ) {
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IndexedFastaSequenceFile reference = new IndexedFastaSequenceFile(referenceFile);
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String expectedRef = new String(reference.getSubsequenceAt(reference.getSequenceDictionary().getSequences().get(0).getSequenceName(),read.getAlignmentStart(),read.getAlignmentStart()+read.getReadLength()-1).getBases());
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int expectedMismatches = 0;
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for( int i = 0; i < read.getReadLength(); i++ ) {
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if( read.getReadBases()[i] != expectedRef.charAt(i) )
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expectedMismatches++;
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}
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String alignedRef = new String(reference.getSubsequenceAt(reference.getSequenceDictionary().getSequences().get(0).getSequenceName(),alignments.get(0).getAlignmentStart(),alignments.get(0).getAlignmentStart()+read.getReadLength()-1).getBases());
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int actualMismatches = 0;
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for( int i = 0; i < read.getReadLength(); i++ ) {
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if( read.getReadBases()[i] != alignedRef.charAt(i) )
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actualMismatches++;
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}
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if( expectedMismatches != actualMismatches ) {
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System.out.printf("read = %s%n", read.getReadString());
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System.out.printf("expected ref = %s%n", expectedRef);
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System.out.printf("actual ref = %s%n", alignedRef);
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throw new StingException(String.format("Read %s was placed at incorrect location; target alignment = %d; actual alignment = %d%n",read.getReadName(),read.getAlignmentStart(),alignment.getAlignmentStart()));
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}
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}
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if( count % 1000 == 0 )
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System.out.printf("%d reads examined.%n",count);
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}
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System.out.printf("%d reads examined.%n",count);
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}
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}
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