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Support negative strand alignments. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1748 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-09-30 18:10:26 +00:00
parent d3b1732cca
commit 665951f9f0
2 changed files with 60 additions and 26 deletions
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46
java/src/org/broadinstitute/sting/alignment/bwa/AlignerTestHarness.java
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@ -4,6 +4,7 @@ import org.broadinstitute.sting.alignment.bwa.bwt.*;
import org.broadinstitute.sting.alignment.Aligner; import org.broadinstitute.sting.alignment.Aligner;
import org.broadinstitute.sting.alignment.Alignment; import org.broadinstitute.sting.alignment.Alignment;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile; import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
import java.io.File; import java.io.File;
@ -21,24 +22,23 @@ import net.sf.samtools.SAMFileReader;
*/ */
public class AlignerTestHarness { public class AlignerTestHarness {
public static void main( String argv[] ) throws FileNotFoundException { public static void main( String argv[] ) throws FileNotFoundException {
if( argv.length != 5 ) { if( argv.length != 6 ) {
System.out.println("PerfectAlignerTestHarness <fasta> <bwt> <rbwt> <sa> <bam>"); System.out.println("PerfectAlignerTestHarness <fasta> <bwt> <rbwt> <sa> <rsa> <bam>");
System.exit(1); System.exit(1);
} }
File referenceFile = new File(argv[0]); File referenceFile = new File(argv[0]);
File bwtFile = new File(argv[1]); File bwtFile = new File(argv[1]);
File rbwtFile = new File(argv[2]); File rbwtFile = new File(argv[2]);
File reverseSuffixArrayFile = new File(argv[3]); File suffixArrayFile = new File(argv[3]);
File bamFile = new File(argv[4]); File reverseSuffixArrayFile = new File(argv[4]);
File bamFile = new File(argv[5]);
align(referenceFile,bwtFile,rbwtFile,reverseSuffixArrayFile,bamFile); align(referenceFile,bwtFile,rbwtFile,suffixArrayFile,reverseSuffixArrayFile,bamFile);
} }
private static void align(File referenceFile, File bwtFile, File rbwtFile, File reverseSuffixArrayFile, File bamFile) throws FileNotFoundException { private static void align(File referenceFile, File bwtFile, File rbwtFile, File suffixArrayFile, File reverseSuffixArrayFile, File bamFile) throws FileNotFoundException {
BWT bwt = new BWTReader(bwtFile).read(); Aligner aligner = new BWAAligner(bwtFile,rbwtFile,suffixArrayFile,reverseSuffixArrayFile);
Aligner aligner = new BWAAligner(bwtFile,rbwtFile,reverseSuffixArrayFile);
int count = 0; int count = 0;
SAMFileReader reader = new SAMFileReader(bamFile); SAMFileReader reader = new SAMFileReader(bamFile);
@ -46,12 +46,31 @@ public class AlignerTestHarness {
for(SAMRecord read: reader) { for(SAMRecord read: reader) {
count++; count++;
//if( count > 39 ) break; //if( count > 25000 ) break;
//if( count != 39 ) continue; //if( count != 39 ) continue;
//if( !read.getReadName().endsWith("1507:1636#0") ) //if( !read.getReadName().endsWith("1507:1636#0") )
// continue; // continue;
List<Alignment> alignments = aligner.align(read); SAMRecord alignmentCleaned = null;
try {
alignmentCleaned = (SAMRecord)read.clone();
}
catch( CloneNotSupportedException ex ) {
throw new StingException("SAMRecord clone not supported", ex);
}
if( alignmentCleaned.getReadNegativeStrandFlag() )
alignmentCleaned.setReadBases(BaseUtils.simpleReverseComplement(alignmentCleaned.getReadBases()));
alignmentCleaned.setReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
alignmentCleaned.setAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
alignmentCleaned.setMappingQuality(SAMRecord.NO_MAPPING_QUALITY);
alignmentCleaned.setCigarString(SAMRecord.NO_ALIGNMENT_CIGAR);
// Clear everything except flags pertaining to pairing and set 'unmapped' status to true.
alignmentCleaned.setFlags(alignmentCleaned.getFlags() & 0x00A1 | 0x000C);
List<Alignment> alignments = aligner.align(alignmentCleaned);
if(alignments.size() == 0 ) if(alignments.size() == 0 )
throw new StingException(String.format("Unable to align read %s to reference; count = %d",read.getReadName(),count)); throw new StingException(String.format("Unable to align read %s to reference; count = %d",read.getReadName(),count));
@ -59,6 +78,9 @@ public class AlignerTestHarness {
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()); 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());
if( read.getReadNegativeStrandFlag() != alignment.isNegativeStrand() )
throw new StingException("Read has been aligned in wrong direction");
if( read.getAlignmentStart() != alignment.getAlignmentStart() ) { if( read.getAlignmentStart() != alignment.getAlignmentStart() ) {
IndexedFastaSequenceFile reference = new IndexedFastaSequenceFile(referenceFile); IndexedFastaSequenceFile reference = new IndexedFastaSequenceFile(referenceFile);
String expectedRef = new String(reference.getSubsequenceAt(reference.getSequenceDictionary().getSequences().get(0).getSequenceName(),read.getAlignmentStart(),read.getAlignmentStart()+read.getReadLength()-1).getBases()); String expectedRef = new String(reference.getSubsequenceAt(reference.getSequenceDictionary().getSequences().get(0).getSequenceName(),read.getAlignmentStart(),read.getAlignmentStart()+read.getReadLength()-1).getBases());
@ -71,7 +93,7 @@ public class AlignerTestHarness {
String alignedRef = new String(reference.getSubsequenceAt(reference.getSequenceDictionary().getSequences().get(0).getSequenceName(),alignments.get(0).getAlignmentStart(),alignments.get(0).getAlignmentStart()+read.getReadLength()-1).getBases()); String alignedRef = new String(reference.getSubsequenceAt(reference.getSequenceDictionary().getSequences().get(0).getSequenceName(),alignments.get(0).getAlignmentStart(),alignments.get(0).getAlignmentStart()+read.getReadLength()-1).getBases());
int actualMismatches = 0; int actualMismatches = 0;
for( int i = 0; i < read.getReadLength(); i++ ) { for( int i = 0; i < read.getReadLength(); i++ ) {
if( read.getReadBases()[i] != expectedRef.charAt(i) ) if( read.getReadBases()[i] != alignedRef.charAt(i) )
actualMismatches++; actualMismatches++;
} }

40
java/src/org/broadinstitute/sting/alignment/bwa/BWAAligner.java
View File

@ -30,6 +30,11 @@ public class BWAAligner implements Aligner {
/** /**
* Suffix array in the forward direction. * Suffix array in the forward direction.
*/ */
private SuffixArray forwardSuffixArray;
/**
* Suffix array in the reverse direction.
*/
private SuffixArray reverseSuffixArray; private SuffixArray reverseSuffixArray;
/** /**
@ -62,41 +67,47 @@ public class BWAAligner implements Aligner {
*/ */
public final int GAP_EXTENSION_PENALTY = 4; public final int GAP_EXTENSION_PENALTY = 4;
public BWAAligner( File forwardBWTFile, File reverseBWTFile, File reverseSuffixArrayFile ) { public BWAAligner( File forwardBWTFile, File reverseBWTFile, File forwardSuffixArrayFile, File reverseSuffixArrayFile ) {
forwardBWT = new BWTReader(forwardBWTFile).read(); forwardBWT = new BWTReader(forwardBWTFile).read();
reverseBWT = new BWTReader(reverseBWTFile).read(); reverseBWT = new BWTReader(reverseBWTFile).read();
forwardSuffixArray = new SuffixArrayReader(forwardSuffixArrayFile).read();
reverseSuffixArray = new SuffixArrayReader(reverseSuffixArrayFile).read(); reverseSuffixArray = new SuffixArrayReader(reverseSuffixArrayFile).read();
} }
public List<Alignment> align( SAMRecord read ) { public List<Alignment> align( SAMRecord read ) {
byte[] forwardBases = read.getReadBases(); byte[] uncomplementedBases = read.getReadBases();
byte[] reverseBases = BaseUtils.simpleReverseComplement(forwardBases); byte[] complementedBases = BaseUtils.reverse(BaseUtils.simpleReverseComplement(uncomplementedBases));
List<LowerBound> forwardLowerBounds = LowerBound.create(forwardBases,forwardBWT); List<LowerBound> forwardLowerBounds = LowerBound.create(uncomplementedBases,forwardBWT);
List<LowerBound> reverseLowerBounds = LowerBound.create(reverseBases,reverseBWT); List<LowerBound> reverseLowerBounds = LowerBound.create(complementedBases,reverseBWT);
//for( int i = 0; i < forwardLowerBounds.size(); i++ ) /*
// System.out.printf("ForwardBWT: lb[%d] = %s%n",i,forwardLowerBounds.get(i)); for( int i = 0; i < forwardLowerBounds.size(); i++ )
//for( int i = 0; i < reverseLowerBounds.size(); i++ ) System.out.printf("ForwardBWT: lb[%d] = %s%n",i,forwardLowerBounds.get(i));
// System.out.printf("ReverseBWT: lb[%d] = %s%n",i,reverseLowerBounds.get(i)); for( int i = 0; i < reverseLowerBounds.size(); i++ )
System.out.printf("ReverseBWT: lb[%d] = %s%n",i,reverseLowerBounds.get(i));
*/
PriorityQueue<BWAAlignment> alignments = new PriorityQueue<BWAAlignment>(); PriorityQueue<BWAAlignment> alignments = new PriorityQueue<BWAAlignment>();
// Create a fictional initial alignment, with the position just off the end of the read, and the limits // Create a fictional initial alignment, with the position just off the end of the read, and the limits
// set as the entire BWT. // set as the entire BWT.
alignments.add(createSeedAlignment(forwardBWT)); alignments.add(createSeedAlignment(forwardBWT));
//alignments.add(createSeedAlignment(reverseBWT)); alignments.add(createSeedAlignment(reverseBWT));
while(!alignments.isEmpty()) { while(!alignments.isEmpty()) {
BWAAlignment alignment = alignments.remove(); BWAAlignment alignment = alignments.remove();
byte[] bases = alignment.negativeStrand ? forwardBases : reverseBases; byte[] bases = alignment.negativeStrand ? complementedBases : uncomplementedBases;
BWT bwt = alignment.negativeStrand ? reverseBWT : forwardBWT; BWT bwt = alignment.negativeStrand ? forwardBWT : reverseBWT;
List<LowerBound> lowerBounds = alignment.negativeStrand ? forwardLowerBounds : reverseLowerBounds; List<LowerBound> lowerBounds = alignment.negativeStrand ? reverseLowerBounds : forwardLowerBounds;
// Done with this particular alignment. // Done with this particular alignment.
if(alignment.position == read.getReadLength()-1) { if(alignment.position == read.getReadLength()-1) {
alignment.alignmentStart = reverseBWT.length() - (reverseSuffixArray.get(alignment.loBound)+read.getReadLength()-alignment.gapOpens-alignment.gapExtensions) + 1; if( !alignment.isNegativeStrand() )
alignment.alignmentStart = reverseBWT.length() - (reverseSuffixArray.get(alignment.loBound)+read.getReadLength()-alignment.gapOpens-alignment.gapExtensions) + 1;
else
alignment.alignmentStart = forwardSuffixArray.get(alignment.loBound) + 1;
return Collections.<Alignment>singletonList(alignment); return Collections.<Alignment>singletonList(alignment);
} }
@ -211,6 +222,7 @@ public class BWAAligner implements Aligner {
/** /**
* Create new alignments representing a deletion a this point in the read. * Create new alignments representing a deletion a this point in the read.
* @param bwt source BWT for inferring deletion info.
* @param alignment Alignment from which to derive the deletion. * @param alignment Alignment from which to derive the deletion.
* @return New alignments reflecting all possible deletions. * @return New alignments reflecting all possible deletions.
*/ */