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Fixed bug where not all alignments were returned if read aligned to multiple locations. Enhanced test suite to validate all alignments. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1762 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-10-04 18:20:20 +00:00
parent 05aa928e3e
commit 56bc4fa21a
3 changed files with 48 additions and 45 deletions
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67
java/src/org/broadinstitute/sting/alignment/bwa/AlignerTestHarness.java
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@ -43,13 +43,14 @@ public class AlignerTestHarness {
SAMFileReader reader = new SAMFileReader(bamFile);
reader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
int mismatches = 0;
int mismatches = 0;
int failures = 0;
for(SAMRecord read: reader) {
count++;
if( count > 10000 ) break;
//if( count > 100000 ) break;
//if( count != 2 ) continue;
//if( !read.getReadName().endsWith("1507:1636#0") )
//if( !read.getReadName().endsWith("SL-XBC:1:90:15:1280#0") )
// continue;
SAMRecord alignmentCleaned = null;
@ -72,48 +73,46 @@ public class AlignerTestHarness {
alignmentCleaned.setFlags(alignmentCleaned.getFlags() & 0x00A1 | 0x000C);
List<Alignment> alignments = aligner.align(alignmentCleaned);
if(alignments.size() == 0 )
throw new StingException(String.format("Unable to align read %s to reference; count = %d",read.getReadName(),count));
Alignment alignment = alignments.get(0);
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() ) {
System.out.println("Read has been aligned in wrong direction");
mismatches++;
if(alignments.size() == 0 ) {
//throw new StingException(String.format("Unable to align read %s to reference; count = %d",read.getReadName(),count));
System.out.printf("Unable to align read %s to reference; count = %d%n",read.getReadName(),count);
failures++;
}
if( read.getAlignmentStart() != alignment.getAlignmentStart() ) {
Alignment foundAlignment = null;
for( Alignment alignment: alignments ) {
if( read.getReadNegativeStrandFlag() != alignment.isNegativeStrand() )
continue;
if( read.getAlignmentStart() != alignment.getAlignmentStart() )
continue;
foundAlignment = alignment;
}
if( foundAlignment != null ) {
//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 {
mismatches++;
//throw new StingException(String.format("Read %s was placed at incorrect location; target alignment = %d; actual alignment = %d; count = %d%n",read.getReadName(),read.getAlignmentStart(),alignment.getAlignmentStart(),count));
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());
int expectedMismatches = 0;
for( int i = 0; i < read.getReadLength(); i++ ) {
if( read.getReadBases()[i] != expectedRef.charAt(i) )
expectedMismatches++;
}
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;
for( int i = 0; i < read.getReadLength(); i++ ) {
if( read.getReadBases()[i] != alignedRef.charAt(i) )
actualMismatches++;
}
if( expectedMismatches != actualMismatches ) {
System.out.printf("read = %s%n", read.getReadString());
System.out.printf("expected ref = %s%n", expectedRef);
System.out.printf("actual ref = %s%n", alignedRef);
mismatches++;
//throw new StingException(String.format("Read %s was placed at incorrect location; target alignment = %d; actual alignment = %d; count = %d%n",read.getReadName(),read.getAlignmentStart(),alignment.getAlignmentStart(),count));
System.out.printf("read = %s, strand = %b%n", read.getReadString(), read.getReadNegativeStrandFlag());
System.out.printf("expected ref = %s%n", expectedRef);
for( Alignment alignment: alignments ) {
String alignedRef = new String(reference.getSubsequenceAt(reference.getSequenceDictionary().getSequences().get(0).getSequenceName(),alignments.get(0).getAlignmentStart(),alignments.get(0).getAlignmentStart()+read.getReadLength()-1).getBases());
System.out.printf("actual ref = %s, strand = %b%n", alignedRef, read.getReadNegativeStrandFlag());
//System.out.printf("(reversed) = %s, strand = %b%n", BaseUtils.simpleReverseComplement(alignedRef), !read.getReadNegativeStrandFlag());
}
}
if( count % 1000 == 0 )
System.out.printf("%d reads examined.%n",count);
}
System.out.printf("%d reads examined; %d mismatches.%n",count,mismatches);
System.out.printf("%d reads examined; %d mismatches; %d failures.%n",count,mismatches,failures);
}
}

24
java/src/org/broadinstitute/sting/alignment/bwa/BWAAligner.java
View File

@ -120,17 +120,21 @@ public class BWAAligner implements Aligner {
// Found a valid alignment; store it and move on.
if(alignment.position == read.getReadLength()-1) {
if( !alignment.isNegativeStrand() ) {
int sizeAlongReference = alignment.getNumberOfBasesMatchingState(AlignmentState.MATCH_MISMATCH)+alignment.getNumberOfBasesMatchingState(AlignmentState.DELETION);
alignment.alignmentStart = reverseBWT.length() - reverseSuffixArray.get(alignment.loBound) - sizeAlongReference + 1;
}
else
alignment.alignmentStart = forwardSuffixArray.get(alignment.loBound) + 1;
successfulMatches.add(alignment);
for( int bwtIndex = alignment.loBound; bwtIndex <= alignment.hiBound; bwtIndex++ ) {
BWAAlignment finalAlignment = alignment.clone();
bestScore = Math.min(alignment.getScore(),bestScore);
bestDiff = Math.min(alignment.mismatches+alignment.gapOpens+alignment.gapExtensions,bestDiff);
maxDiff = bestDiff + 1;
if( finalAlignment.isNegativeStrand() )
finalAlignment.alignmentStart = forwardSuffixArray.get(bwtIndex) + 1;
else {
int sizeAlongReference = finalAlignment.getNumberOfBasesMatchingState(AlignmentState.MATCH_MISMATCH)+finalAlignment.getNumberOfBasesMatchingState(AlignmentState.DELETION);
finalAlignment.alignmentStart = reverseBWT.length() - reverseSuffixArray.get(bwtIndex) - sizeAlongReference + 1;
}
successfulMatches.add(finalAlignment);
bestScore = Math.min(finalAlignment.getScore(),bestScore);
bestDiff = Math.min(finalAlignment.mismatches+finalAlignment.gapOpens+finalAlignment.gapExtensions,bestDiff);
maxDiff = bestDiff + 1;
}
continue;
}

2
java/src/org/broadinstitute/sting/alignment/bwa/BWAAlignment.java
View File

@ -168,6 +168,6 @@ public class BWAAlignment implements Alignment, Cloneable {
}
public String toString() {
return String.format("position: %d, state: %s, mismatches: %d, gap opens: %d, gap extensions: %d, loBound: %d, hiBound: %d, score: %d, creationNumber: %d", position, alignmentMatchSequence.getCurrentState(), mismatches, gapOpens, gapExtensions, loBound, hiBound, getScore(), creationNumber);
return String.format("position: %d, strand: %b, state: %s, mismatches: %d, gap opens: %d, gap extensions: %d, loBound: %d, hiBound: %d, score: %d, creationNumber: %d", position, negativeStrand, alignmentMatchSequence.getCurrentState(), mismatches, gapOpens, gapExtensions, loBound, hiBound, getScore(), creationNumber);
}
}