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Our BWA is now looking at roughly the same number of candidate alignments as BWA/C. Performance is now at 11k reads / min, still a long way from BWA/C. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1817 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-10-13 15:50:04 +00:00
parent 8d0e057d83
commit f37564e63a
2 changed files with 55 additions and 22 deletions
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6
java/src/org/broadinstitute/sting/alignment/bwa/AlignerTestHarness.java
View File

@ -47,8 +47,8 @@ public class AlignerTestHarness {
for(SAMRecord read: reader) {
count++;
//if( count > 144000 ) break;
if( count < 366000 ) continue;
//if( count > 100000 ) break;
//if( count < 366000 ) continue;
//if( count != 2 ) continue;
//if( !read.getReadName().endsWith("SL-XBC:1:82:506:404#0") )
// continue;
@ -95,6 +95,8 @@ 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(), foundAlignment.getAlignmentStart(), foundAlignment.getMismatches(), foundAlignment.getGapOpens(), foundAlignment.getGapExtensions());
}
else {
System.out.printf("Error aligning read %s%n", read.getReadName());
mismatches++;
IndexedFastaSequenceFile reference = new IndexedFastaSequenceFile(referenceFile);

71
java/src/org/broadinstitute/sting/alignment/bwa/BWAAligner.java
View File

@ -88,13 +88,6 @@ public class BWAAligner implements Aligner {
List<LowerBound> forwardLowerBounds = LowerBound.create(uncomplementedBases,forwardBWT);
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 < reverseLowerBounds.size(); i++ )
System.out.printf("ReverseBWT: lb[%d] = %s%n",i,reverseLowerBounds.get(i));
*/
// Seed the best score with any score that won't overflow on comparison.
int bestScore = Integer.MAX_VALUE - MISMATCH_PENALTY;
int bestDiff = MAXIMUM_EDIT_DISTANCE+1;
@ -118,8 +111,19 @@ public class BWAAligner implements Aligner {
BWT bwt = alignment.negativeStrand ? forwardBWT : reverseBWT;
List<LowerBound> lowerBounds = alignment.negativeStrand ? reverseLowerBounds : forwardLowerBounds;
// if z < D(i) then return {}
int mismatches = maxDiff - alignment.mismatches - alignment.gapOpens - alignment.gapExtensions;
if( alignment.position < lowerBounds.size()-1 && mismatches < lowerBounds.get(alignment.position+1).value )
continue;
if(mismatches == 0) {
exactMatch(alignment,bases,bwt);
if(alignment.loBound > alignment.hiBound)
continue;
}
// Found a valid alignment; store it and move on.
if(alignment.position == read.getReadLength()-1) {
if(alignment.position >= read.getReadLength()-1) {
for( int bwtIndex = alignment.loBound; bwtIndex <= alignment.hiBound; bwtIndex++ ) {
BWAAlignment finalAlignment = alignment.clone();
@ -143,13 +147,31 @@ public class BWAAligner implements Aligner {
}
//System.out.printf("Processing alignments; queue size = %d, alignment = %s, bound = %d, base = %s%n", alignments.size(), alignment, lowerBounds.get(alignment.position+1).value, alignment.position >= 0 ? (char)bases[alignment.position] : "");
/*
System.out.printf("#1\t[%d,%d,%d,%c]\t[%d,%d,%d]\t[%d,%d]\t[%d,%d]%n",alignments.size(),
alignment.negativeStrand?1:0,
bases.length-alignment.position-1,
alignment.getCurrentState().toString().charAt(0),
alignment.getMismatches(),
alignment.getGapOpens(),
alignment.getGapExtensions(),
lowerBounds.get(alignment.position+1).value,
lowerBounds.get(alignment.position+1).width,
alignment.loBound,
alignment.hiBound);
*/
// if z < D(i) then return {}
int mismatches = maxDiff - alignment.mismatches - alignment.gapOpens - alignment.gapExtensions;
if( mismatches < lowerBounds.get(alignment.position+1).value )
continue;
// Temporary -- look ahead to see if the next alignment is bounded.
boolean allowDifferences = mismatches > 0;
boolean allowMismatches = mismatches > 0;
if( alignment.position+1 < read.getReadLength()-1 ) {
allowDifferences &= lowerBounds.get(alignment.position+2).value <= mismatches - 1;
allowMismatches &=
!(lowerBounds.get(alignment.position+2).value == mismatches-1 && lowerBounds.get(alignment.position+1).value == mismatches-1 &&
lowerBounds.get(alignment.position+2).width == lowerBounds.get(alignment.position+1).width);
}
if( mismatches > 0 &&
if( allowDifferences &&
alignment.position+1 >= INDEL_END_SKIP-1+alignment.gapOpens+alignment.gapExtensions &&
read.getReadLength()-1-(alignment.position+1) >= INDEL_END_SKIP+alignment.gapOpens+alignment.gapExtensions ) {
if( alignment.getCurrentState() == AlignmentState.MATCH_MISMATCH ) {
@ -186,13 +208,7 @@ public class BWAAligner implements Aligner {
}
// Mismatches
// Temporary -- look ahead to see if the next alignment is bounded.
boolean allowMismatches = mismatches > 0;
if( alignment.position+1 < read.getReadLength()-1 )
allowMismatches &=
!(lowerBounds.get(alignment.position+2).value == mismatches-1 && lowerBounds.get(alignment.position+1).value == mismatches-1 &&
lowerBounds.get(alignment.position+2).width == lowerBounds.get(alignment.position+1).width);
alignments.addAll(createMatchedAlignments(bwt,alignment,bases,allowMismatches));
alignments.addAll(createMatchedAlignments(bwt,alignment,bases,allowDifferences&&allowMismatches));
}
return successfulMatches;
@ -302,4 +318,19 @@ public class BWAAligner implements Aligner {
return newAlignments;
}
/**
* Exactly match the given alignment against the given BWT.
* @param alignment Alignment to match.
* @param bases Bases to use.
* @param bwt BWT to use.
*/
private void exactMatch( BWAAlignment alignment, byte[] bases, BWT bwt ) {
while( ++alignment.position < bases.length ) {
Base base = Base.fromASCII(bases[alignment.position]);
alignment.loBound = bwt.counts(base) + bwt.occurrences(base,alignment.loBound-1) + 1;
alignment.hiBound = bwt.counts(base) + bwt.occurrences(base,alignment.hiBound);
if( alignment.loBound > alignment.hiBound )
return;
}
}
}