77 lines
3.8 KiB
Java
77 lines
3.8 KiB
Java
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package org.broadinstitute.sting.bwa;
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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 java.io.File;
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import java.io.FileNotFoundException;
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import net.sf.picard.reference.ReferenceSequence;
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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 PerfectAlignerTestHarness {
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public static final String[] sampleReads = { "AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGA",
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"AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTAG",
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"GCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGCGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCAGAT",
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"GCTTTTCATTCTGACTGCAACGGGCAATATGTATCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAA",
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"GCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAA",
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"CTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAAC",
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"TTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTACTGAACT",
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"TTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAAGAGTGTCTGATAGCAGCTTCTGAAC",
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"TTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACT",
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"CATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTT"};
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private static BWT bwt;
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private static SuffixArray suffixArray;
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public static void main( String argv[] ) throws FileNotFoundException {
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if( argv.length != 3 ) {
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System.out.println("PerfectAlignerTestHarness <fasta> <bwt> <sa>");
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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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IndexedFastaSequenceFile reference = new IndexedFastaSequenceFile(referenceFile);
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File bwtFile = new File(argv[1]);
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BWTReader reader = new BWTReader(bwtFile);
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bwt = reader.read();
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File suffixArrayFile = new File(argv[2]);
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SuffixArrayReader suffixArrayReader = new SuffixArrayReader(suffixArrayFile);
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suffixArray = suffixArrayReader.read();
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for( String read: sampleReads ) {
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int alignmentStart = align(read);
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if( alignmentStart < 0 ) {
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System.out.printf("Unable to align read %s%n",read);
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continue;
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}
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ReferenceSequence subsequence = reference.getSubsequenceAt(reference.getSequenceDictionary().getSequences().get(0).getSequenceName(),alignmentStart,alignmentStart+read.length()-1);
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for( int i = 0; i < subsequence.length(); i++) {
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if( subsequence.getBases()[i] != read.charAt(i) )
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throw new StingException("Read is not an exact match! Alignment has failed!");
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}
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System.out.printf("Read %s aligned to position %d%n", read, alignmentStart);
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}
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}
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public static int align( String read ) {
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int lowerBound = 0, upperBound = bwt.length();
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for( int i = read.length()-1; i >= 0; i-- ) {
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Base base = Base.fromASCII((byte)read.charAt(i));
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lowerBound = bwt.counts(base) + bwt.occurrences(base,lowerBound-1)+1;
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upperBound = bwt.counts(base) + bwt.occurrences(base,upperBound);
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if( lowerBound > upperBound ) return -1;
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}
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int alignmentStart = suffixArray.sequence[lowerBound]+1;
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//System.out.printf("Read = %s; final bounds: (%d->%d); suffix array = %d%n",read,lowerBound,upperBound,alignmentStart);
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return alignmentStart;
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}
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}
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