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Add in weights. Massive performance improvements. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1722 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-09-24 23:19:15 +00:00
parent 3b79f9eddc
commit 44879c81b0
2 changed files with 40 additions and 12 deletions
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35
java/src/org/broadinstitute/sting/alignment/bwa/BWAAligner.java
View File

@ -38,17 +38,32 @@ public class BWAAligner implements Aligner {
/** /**
* Maximum edit distance (-n option from original BWA). * Maximum edit distance (-n option from original BWA).
*/ */
private static final int MAXIMUM_EDIT_DISTANCE = 4; private final int MAXIMUM_EDIT_DISTANCE = 4;
/** /**
* Maximum number of gap opens (-o option from original BWA). * Maximum number of gap opens (-o option from original BWA).
*/ */
private static final int MAXIMUM_GAP_OPENS = 1; private final int MAXIMUM_GAP_OPENS = 1;
/** /**
* Maximum number of gap extensions (-e option from original BWA). * Maximum number of gap extensions (-e option from original BWA).
*/ */
private static final int MAXIMUM_GAP_EXTENSIONS = 6; private final int MAXIMUM_GAP_EXTENSIONS = 6;
/**
* Penalty for straight mismatches (-M option from original BWA).
*/
public final int MISMATCH_PENALTY = 3;
/**
* Penalty for gap opens (-O option from original BWA).
*/
public final int GAP_OPEN_PENALTY = 11;
/**
* Penalty for gap extensions (-E option from original BWA).
*/
public final int GAP_EXTENSION_PENALTY = 4;
public BWAAligner( File forwardBWTFile, File reverseBWTFile, File reverseSuffixArrayFile ) { public BWAAligner( File forwardBWTFile, File reverseBWTFile, File reverseSuffixArrayFile ) {
forwardBWT = new BWTReader(forwardBWTFile).read(); forwardBWT = new BWTReader(forwardBWTFile).read();
@ -71,7 +86,7 @@ public class BWAAligner implements Aligner {
// 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.
BWAAlignment initial = new BWAAlignment(); BWAAlignment initial = new BWAAlignment(this);
initial.negativeStrand = true; initial.negativeStrand = true;
initial.position = 0; initial.position = 0;
initial.loBound = 0; initial.loBound = 0;
@ -79,7 +94,7 @@ public class BWAAligner implements Aligner {
initial.state = AlignmentState.MATCH_MISMATCH; initial.state = AlignmentState.MATCH_MISMATCH;
initial.mismatches = 0; initial.mismatches = 0;
BWAAlignment initialReverse = new BWAAlignment(); BWAAlignment initialReverse = new BWAAlignment(this);
initialReverse.negativeStrand = false; initialReverse.negativeStrand = false;
initialReverse.position = 0; initialReverse.position = 0;
initialReverse.loBound = 0; initialReverse.loBound = 0;
@ -116,7 +131,7 @@ public class BWAAligner implements Aligner {
if( alignment.state == AlignmentState.MATCH_MISMATCH ) { if( alignment.state == AlignmentState.MATCH_MISMATCH ) {
if( alignment.gapOpens < MAXIMUM_GAP_OPENS ) { if( alignment.gapOpens < MAXIMUM_GAP_OPENS ) {
// Add a potential insertion. // Add a potential insertion.
BWAAlignment newAlignment = new BWAAlignment(); BWAAlignment newAlignment = new BWAAlignment(this);
newAlignment.negativeStrand = alignment.negativeStrand; newAlignment.negativeStrand = alignment.negativeStrand;
newAlignment.position = alignment.position + 1; newAlignment.position = alignment.position + 1;
newAlignment.state = AlignmentState.INSERTION; newAlignment.state = AlignmentState.INSERTION;
@ -130,7 +145,7 @@ public class BWAAligner implements Aligner {
// Add a potential deletion by marking a deletion and augmenting the position. // Add a potential deletion by marking a deletion and augmenting the position.
for(Base base: EnumSet.allOf(Base.class)) { for(Base base: EnumSet.allOf(Base.class)) {
newAlignment = new BWAAlignment(); newAlignment = new BWAAlignment(this);
newAlignment.negativeStrand = alignment.negativeStrand; newAlignment.negativeStrand = alignment.negativeStrand;
newAlignment.position = alignment.position; newAlignment.position = alignment.position;
newAlignment.state = AlignmentState.DELETION; newAlignment.state = AlignmentState.DELETION;
@ -148,7 +163,7 @@ public class BWAAligner implements Aligner {
else if( alignment.state == AlignmentState.INSERTION ) { else if( alignment.state == AlignmentState.INSERTION ) {
if( alignment.gapExtensions < MAXIMUM_GAP_EXTENSIONS ) { if( alignment.gapExtensions < MAXIMUM_GAP_EXTENSIONS ) {
// Add a potential insertion extension. // Add a potential insertion extension.
BWAAlignment newAlignment = new BWAAlignment(); BWAAlignment newAlignment = new BWAAlignment(this);
newAlignment.negativeStrand = alignment.negativeStrand; newAlignment.negativeStrand = alignment.negativeStrand;
newAlignment.position = alignment.position + 1; newAlignment.position = alignment.position + 1;
newAlignment.state = AlignmentState.INSERTION; newAlignment.state = AlignmentState.INSERTION;
@ -166,7 +181,7 @@ public class BWAAligner implements Aligner {
if( alignment.gapExtensions < MAXIMUM_GAP_EXTENSIONS ) { if( alignment.gapExtensions < MAXIMUM_GAP_EXTENSIONS ) {
// Add a potential deletion by marking a deletion and augmenting the position. // Add a potential deletion by marking a deletion and augmenting the position.
for(Base base: EnumSet.allOf(Base.class)) { for(Base base: EnumSet.allOf(Base.class)) {
BWAAlignment newAlignment = new BWAAlignment(); BWAAlignment newAlignment = new BWAAlignment(this);
newAlignment.negativeStrand = alignment.negativeStrand; newAlignment.negativeStrand = alignment.negativeStrand;
newAlignment.position = alignment.position; newAlignment.position = alignment.position;
newAlignment.state = AlignmentState.DELETION; newAlignment.state = AlignmentState.DELETION;
@ -184,7 +199,7 @@ public class BWAAligner implements Aligner {
// Mismatches // Mismatches
for(Base base: EnumSet.allOf(Base.class)) { for(Base base: EnumSet.allOf(Base.class)) {
// Create and initialize a new alignment, given that base as the candidate. // Create and initialize a new alignment, given that base as the candidate.
BWAAlignment newAlignment = new BWAAlignment(); BWAAlignment newAlignment = new BWAAlignment(this);
newAlignment.negativeStrand = alignment.negativeStrand; newAlignment.negativeStrand = alignment.negativeStrand;
newAlignment.position = alignment.position + 1; newAlignment.position = alignment.position + 1;
newAlignment.state = AlignmentState.MATCH_MISMATCH; newAlignment.state = AlignmentState.MATCH_MISMATCH;

15
java/src/org/broadinstitute/sting/alignment/bwa/BWAAlignment.java
View File

@ -10,6 +10,11 @@ import org.broadinstitute.sting.alignment.Alignment;
* @version 0.1 * @version 0.1
*/ */
public class BWAAlignment implements Alignment { public class BWAAlignment implements Alignment {
/**
* The aligner performing the alignments.
*/
protected BWAAligner aligner;
/** /**
* Start of the final alignment. * Start of the final alignment.
*/ */
@ -76,13 +81,21 @@ public class BWAAlignment implements Alignment {
* @return BWA-style scores. 0 is best. * @return BWA-style scores. 0 is best.
*/ */
public int getScore() { public int getScore() {
return mismatches + gapOpens + gapExtensions; return mismatches*aligner.MISMATCH_PENALTY + gapOpens*aligner.GAP_OPEN_PENALTY + gapExtensions*aligner.GAP_EXTENSION_PENALTY;
} }
public int getMismatches() { return mismatches; } public int getMismatches() { return mismatches; }
public int getGapOpens() { return gapOpens; } public int getGapOpens() { return gapOpens; }
public int getGapExtensions() { return gapExtensions; } public int getGapExtensions() { return gapExtensions; }
/**
* Create a new alignment with the given parent aligner.
* @param aligner Aligner being used.
*/
public BWAAlignment( BWAAligner aligner ) {
this.aligner = aligner;
}
/** /**
* Compare this alignment to another alignment. * Compare this alignment to another alignment.
* @param other Other alignment to which to compare. * @param other Other alignment to which to compare.