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Cleanup existing speedups. Minor performance improvements. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1823 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-10-13 21:51:18 +00:00
parent 837ae1d33a
commit a76fac4687
4 changed files with 25 additions and 13 deletions
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2
java/src/org/broadinstitute/sting/alignment/bwa/AlignerTestHarness.java
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@ -47,7 +47,7 @@ public class AlignerTestHarness {
for(SAMRecord read: reader) {
count++;
if( count > 100000 ) break;
if( count > 200000 ) break;
//if( count < 366000 ) continue;
//if( count != 2 ) continue;
//if( !read.getReadName().endsWith("SL-XBC:1:82:506:404#0") )

28
java/src/org/broadinstitute/sting/alignment/bwa/BWAAligner.java
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@ -82,8 +82,8 @@ public class BWAAligner implements Aligner {
public List<Alignment> align( SAMRecord read ) {
List<Alignment> successfulMatches = new ArrayList<Alignment>();
byte[] uncomplementedBases = read.getReadBases();
byte[] complementedBases = BaseUtils.reverse(BaseUtils.simpleReverseComplement(uncomplementedBases));
Byte[] uncomplementedBases = normalizeBases(read.getReadBases());
Byte[] complementedBases = normalizeBases(BaseUtils.reverse(BaseUtils.simpleReverseComplement(read.getReadBases())));
List<LowerBound> forwardLowerBounds = LowerBound.create(uncomplementedBases,forwardBWT);
List<LowerBound> reverseLowerBounds = LowerBound.create(complementedBases,reverseBWT);
@ -107,7 +107,7 @@ public class BWAAligner implements Aligner {
if( alignment.getScore() > bestScore + MISMATCH_PENALTY )
break;
byte[] bases = alignment.negativeStrand ? complementedBases : uncomplementedBases;
Byte[] bases = alignment.negativeStrand ? complementedBases : uncomplementedBases;
BWT bwt = alignment.negativeStrand ? forwardBWT : reverseBWT;
List<LowerBound> lowerBounds = alignment.negativeStrand ? reverseLowerBounds : forwardLowerBounds;
@ -236,11 +236,11 @@ public class BWAAligner implements Aligner {
* @param allowMismatch Should mismatching bases be allowed?
* @return New alignment representing this position if valid; null otherwise.
*/
private List<BWAAlignment> createMatchedAlignments( BWT bwt, BWAAlignment alignment, byte[] bases, boolean allowMismatch ) {
private List<BWAAlignment> createMatchedAlignments( BWT bwt, BWAAlignment alignment, Byte[] bases, boolean allowMismatch ) {
List<BWAAlignment> newAlignments = new ArrayList<BWAAlignment>();
List<Byte> baseChoices = new ArrayList<Byte>();
Byte thisBase = Bases.fromASCII(bases[alignment.position+1]);
Byte thisBase = bases[alignment.position+1];
if( allowMismatch )
baseChoices.addAll(Bases.allOf());
@ -269,7 +269,7 @@ public class BWAAligner implements Aligner {
newAlignment.position++;
newAlignment.addState(AlignmentState.MATCH_MISMATCH);
if( Bases.fromASCII(bases[newAlignment.position]) == null || base != Bases.fromASCII(bases[newAlignment.position]) )
if( bases[newAlignment.position] == null || base != bases[newAlignment.position] )
newAlignment.incrementMismatches();
newAlignments.add(newAlignment);
@ -323,13 +323,25 @@ public class BWAAligner implements Aligner {
* @param bases Bases to use.
* @param bwt BWT to use.
*/
private void exactMatch( BWAAlignment alignment, byte[] bases, BWT bwt ) {
private void exactMatch( BWAAlignment alignment, Byte[] bases, BWT bwt ) {
while( ++alignment.position < bases.length ) {
byte base = Bases.fromASCII(bases[alignment.position]);
byte base = 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;
}
}
/**
* Make each base into A/C/G/T or null if unknown.
* @param bases Base string to normalize.
* @return Array of normalized bases.
*/
private Byte[] normalizeBases( byte[] bases ) {
Byte[] normalBases = new Byte[bases.length];
for(int i = 0; i < bases.length; i++)
normalBases[i] = Bases.fromASCII(bases[i]);
return normalBases;
}
}

4
java/src/org/broadinstitute/sting/alignment/bwa/BWAAlignment.java
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@ -196,8 +196,8 @@ public class BWAAlignment implements Alignment, Cloneable {
return score > other.score ? 1 : -1;
// Otherwise, use the order in which the elements were created.
if(this.creationNumber != other.creationNumber)
return this.creationNumber > other.creationNumber ? -1 : 1;
if(creationNumber != other.creationNumber)
return creationNumber > other.creationNumber ? -1 : 1;
return 0;
}

4
java/src/org/broadinstitute/sting/alignment/bwa/LowerBound.java
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@ -48,12 +48,12 @@ public class LowerBound {
/**
* Create a non-optimal bound according to the algorithm specified in Figure 3 of the BWA paper.
*/
public static List<LowerBound> create( byte[] bases, BWT bwt ) {
public static List<LowerBound> create( Byte[] bases, BWT bwt ) {
List<LowerBound> bounds = new ArrayList<LowerBound>();
int loIndex = 0, hiIndex = bwt.length(), mismatches = 0;
for( int i = bases.length-1; i >= 0; i-- ) {
Byte base = Bases.fromASCII(bases[i]);
Byte base = bases[i];
// Ignore non-ACGT bases.
if( base != null ) {