zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

67
java/src/org/broadinstitute/sting/alignment/bwa/AlignerTestHarness.java
View File

@ -43,13 +43,14 @@ public class AlignerTestHarness {
SAMFileReader reader = new SAMFileReader(bamFile); SAMFileReader reader = new SAMFileReader(bamFile);
reader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT); reader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
int mismatches = 0; int mismatches = 0;
int failures = 0;
for(SAMRecord read: reader) { for(SAMRecord read: reader) {
count++; count++;
if( count > 10000 ) break; //if( count > 100000 ) break;
//if( count != 2 ) continue; //if( count != 2 ) continue;
//if( !read.getReadName().endsWith("1507:1636#0") ) //if( !read.getReadName().endsWith("SL-XBC:1:90:15:1280#0") )
// continue; // continue;
SAMRecord alignmentCleaned = null; SAMRecord alignmentCleaned = null;
@ -72,48 +73,46 @@ public class AlignerTestHarness {
alignmentCleaned.setFlags(alignmentCleaned.getFlags() & 0x00A1 | 0x000C); alignmentCleaned.setFlags(alignmentCleaned.getFlags() & 0x00A1 | 0x000C);
List<Alignment> alignments = aligner.align(alignmentCleaned); 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));
System.out.printf("Unable to align read %s to reference; count = %d%n",read.getReadName(),count);
Alignment alignment = alignments.get(0); failures++;
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( 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); 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());
int expectedMismatches = 0; System.out.printf("read = %s, strand = %b%n", read.getReadString(), read.getReadNegativeStrandFlag());
for( int i = 0; i < read.getReadLength(); i++ ) { System.out.printf("expected ref = %s%n", expectedRef);
if( read.getReadBases()[i] != expectedRef.charAt(i) ) for( Alignment alignment: alignments ) {
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());
} 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());
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));
} }
} }
if( count % 1000 == 0 ) if( count % 1000 == 0 )
System.out.printf("%d reads examined.%n",count); 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. // Found a valid alignment; store it and move on.
if(alignment.position == read.getReadLength()-1) { if(alignment.position == read.getReadLength()-1) {
if( !alignment.isNegativeStrand() ) { for( int bwtIndex = alignment.loBound; bwtIndex <= alignment.hiBound; bwtIndex++ ) {
int sizeAlongReference = alignment.getNumberOfBasesMatchingState(AlignmentState.MATCH_MISMATCH)+alignment.getNumberOfBasesMatchingState(AlignmentState.DELETION); BWAAlignment finalAlignment = alignment.clone();
alignment.alignmentStart = reverseBWT.length() - reverseSuffixArray.get(alignment.loBound) - sizeAlongReference + 1;
}
else
alignment.alignmentStart = forwardSuffixArray.get(alignment.loBound) + 1;
successfulMatches.add(alignment);
bestScore = Math.min(alignment.getScore(),bestScore); if( finalAlignment.isNegativeStrand() )
bestDiff = Math.min(alignment.mismatches+alignment.gapOpens+alignment.gapExtensions,bestDiff); finalAlignment.alignmentStart = forwardSuffixArray.get(bwtIndex) + 1;
maxDiff = bestDiff + 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; 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() { 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);
} }
} }