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Misc bug fixes. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2501 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-01-05 14:48:19 +00:00
parent 9fb6533549
commit a4b69d0adf
6 changed files with 94 additions and 22 deletions
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7
java/src/org/broadinstitute/sting/alignment/bwa/BWAAligner.java
View File

@ -30,13 +30,6 @@ public abstract class BWAAligner implements Aligner {
this.configuration = configuration;
}
/**
* Close the existing aligner, freeing resources it consumed.
*/
public void close() {
bwtFiles.close();
}
/**
* Update the configuration passed to the BWA aligner.
* @param configuration New configuration to set.

14
java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java
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@ -39,6 +39,11 @@ public class BWTFiles {
*/
public final File pacFile;
/**
* Reverse of packed reference sequence file.
*/
public final File rpacFile;
/**
* Forward BWT file.
*/
@ -62,7 +67,7 @@ public class BWTFiles {
/**
* Where these files autogenerated on the fly?
*/
private final boolean autogenerated;
public final boolean autogenerated;
/**
* Create a new BWA configuration file using the given prefix.
@ -74,6 +79,7 @@ public class BWTFiles {
annFile = new File(prefix + ".ann");
ambFile = new File(prefix + ".amb");
pacFile = new File(prefix + ".pac");
rpacFile = new File(prefix + ".rpac");
forwardBWTFile = new File(prefix + ".bwt");
forwardSAFile = new File(prefix + ".sa");
reverseBWTFile = new File(prefix + ".rbwt");
@ -88,6 +94,7 @@ public class BWTFiles {
* @param pacFile Packed representation of the forward reference sequence.
* @param forwardBWTFile BWT representation of the forward reference sequence.
* @param forwardSAFile SA representation of the forward reference sequence.
* @param rpacFile Packed representation of the reversed reference sequence.
* @param reverseBWTFile BWT representation of the reversed reference sequence.
* @param reverseSAFile SA representation of the reversed reference sequence.
*/
@ -96,6 +103,7 @@ public class BWTFiles {
File pacFile,
File forwardBWTFile,
File forwardSAFile,
File rpacFile,
File reverseBWTFile,
File reverseSAFile) {
this.annFile = annFile;
@ -103,6 +111,7 @@ public class BWTFiles {
this.pacFile = pacFile;
this.forwardBWTFile = forwardBWTFile;
this.forwardSAFile = forwardSAFile;
this.rpacFile = rpacFile;
this.reverseBWTFile = reverseBWTFile;
this.reverseSAFile = reverseSAFile;
autogenerated = true;
@ -120,6 +129,7 @@ public class BWTFiles {
success &= pacFile.delete();
success &= forwardBWTFile.delete();
success &= forwardSAFile.delete();
success &= rpacFile.delete();
success &= reverseBWTFile.delete();
success &= reverseSAFile.delete();
@ -185,7 +195,7 @@ public class BWTFiles {
rbwtFile.deleteOnExit();
rsaFile.deleteOnExit();
return new BWTFiles(annFile,ambFile,pacFile,bwtFile,saFile,rbwtFile,rsaFile);
return new BWTFiles(annFile,ambFile,pacFile,bwtFile,saFile,rpacFile,rbwtFile,rsaFile);
}
/**

9
java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java
View File

@ -48,7 +48,9 @@ public class BWACAligner extends BWAAligner {
* @param configuration Configuration for the given aligner.
*/
public BWACAligner(byte[] referenceSequence, BWAConfiguration configuration) {
this(BWTFiles.createFromReferenceSequence(referenceSequence),configuration);
this(BWTFiles.createFromReferenceSequence(referenceSequence),configuration);
// Now that the temporary files are created, the temporary files can be destroyed.
bwtFiles.close();
}
/**
@ -70,7 +72,6 @@ public class BWACAligner extends BWAAligner {
if(thunkPointer == 0)
throw new StingException("BWA/C close attempted, but BWA/C is not properly initialized.");
destroy(thunkPointer);
super.close();
}
/**
@ -93,6 +94,8 @@ public class BWACAligner extends BWAAligner {
*/
@Override
public SAMRecord align(final SAMRecord read, final SAMFileHeader newHeader) {
if(bwtFiles.autogenerated)
throw new UnsupportedOperationException("Cannot create target alignment; source contig was generated ad-hoc and is not reliable");
return Alignment.convertToRead(getBestAlignment(read.getReadBases()),read,newHeader);
}
@ -148,6 +151,8 @@ public class BWACAligner extends BWAAligner {
*/
@Override
public Iterable<SAMRecord[]> alignAll(final SAMRecord read, final SAMFileHeader newHeader) {
if(bwtFiles.autogenerated)
throw new UnsupportedOperationException("Cannot create target alignment; source contig was generated ad-hoc and is not reliable");
final Iterable<Alignment[]> alignments = getAllAlignments(read.getReadBases());
return new Iterable<SAMRecord[]>() {
public Iterator<SAMRecord[]> iterator() {

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

@ -87,7 +87,7 @@ public class BWAJavaAligner extends BWAAligner {
*/
@Override
public void close() {
super.close();
throw new UnsupportedOperationException("BWA aligner can't currently be closed.");
}
/**

2
java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java
View File

@ -113,7 +113,7 @@ public class SuffixArray {
// Find the first element in the inverse suffix array.
long inverseSA0 = -1;
for(i = 0; i < sequence.length; i++) {
for(i = 0; i < suffixArray.length; i++) {
if(suffixArray[i] == 0)
inverseSA0 = i;
}

82
java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java
View File

@ -5,13 +5,23 @@ import org.broadinstitute.sting.alignment.bwa.BWAAligner;
import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
import org.broadinstitute.sting.alignment.Alignment;
import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.util.StringUtil;
import net.sf.picard.reference.ReferenceSequence;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.Scanner;
import java.util.SortedSet;
import java.util.TreeMap;
import java.util.SortedMap;
/**
* A walker to experiment with fishing for reads in the GATK. Has very limited utility in its current state.
@ -25,20 +35,74 @@ public class TestReadFishingWalker extends ReadWalker<Integer,Long> {
*/
private BWAAligner aligner;
@Override
public void initialize() {
ReferenceSequence initialBases;
@Argument(fullName="indel_calls",shortName="ic",doc="Indel calls to use to derive custom references",required=true)
private File indelCalls;
@Argument(fullName="buffer_width",shortName="bw",doc="How much reference to extract around the given event",required=false)
private int bufferWidth = 36;
private SortedMap<GenomeLoc,BWAAligner> aligners = new TreeMap<GenomeLoc,BWAAligner>();
@Override
public void initialize() {
long startTime = System.currentTimeMillis();
int numAlignersCreated = 0;
IndexedFastaSequenceFile referenceReader;
FileInputStream indelCallInputStream;
try {
IndexedFastaSequenceFile reader = new IndexedFastaSequenceFile(getToolkit().getArguments().referenceFile);
SAMSequenceRecord firstSequence = reader.getSequenceDictionary().getSequences().get(0);
initialBases = reader.getSubsequenceAt(firstSequence.getSequenceName(),1,100);
referenceReader = new IndexedFastaSequenceFile(getToolkit().getArguments().referenceFile);
indelCallInputStream = new FileInputStream(indelCalls);
}
catch(IOException ex) {
throw new StingException("Unable to load initial bases from reference sequence");
throw new StingException("Unable to load indel calls.");
}
aligner = new BWACAligner(initialBases.getBases(),new BWAConfiguration());
Scanner indelCallReader = new Scanner(indelCallInputStream);
while(indelCallReader.hasNext()) {
String contig = indelCallReader.next();
int eventPos = indelCallReader.nextInt();
int eventLength = indelCallReader.nextInt();
char type = indelCallReader.next().toUpperCase().charAt(0);
byte[] bases = StringUtil.stringToBytes(indelCallReader.next());
String sample = indelCallReader.next();
byte[] revisedReference;
int start,stop;
if(type == 'D') {
start = eventPos-eventLength-bufferWidth;
stop = eventPos+eventLength+bufferWidth;
int eventStart = eventPos - start + 1;
int eventStop = eventStart + eventLength - 1;
ReferenceSequence referenceSequence = referenceReader.getSubsequenceAt(contig,start,stop);
revisedReference = new byte[(stop-start+1) - eventLength];
System.arraycopy(referenceSequence.getBases(),0,revisedReference,0,eventStart);
System.arraycopy(referenceSequence.getBases(),eventStop+1,revisedReference,eventStart,stop-start-eventStop);
}
else if(type == 'I') {
start = eventPos-bufferWidth;
stop = eventPos+bufferWidth;
int eventStart = eventPos - start + 1;
ReferenceSequence referenceSequence = referenceReader.getSubsequenceAt(contig,start,stop);
revisedReference = new byte[(stop-start+1) + eventLength];
System.arraycopy(referenceSequence.getBases(),0,revisedReference,0,bufferWidth+1);
System.arraycopy(bases,0,revisedReference,eventStart,eventLength);
System.arraycopy(referenceSequence.getBases(),eventStart,revisedReference,eventStart+eventLength,bufferWidth);
}
else
throw new StingException("Invalid indel type: " + type);
aligners.put(GenomeLocParser.createGenomeLoc(contig,start,stop),new BWACAligner(revisedReference,new BWAConfiguration()));
if(++numAlignersCreated % 100 == 0)
out.printf("Created %d aligners in %dms%n",++numAlignersCreated,System.currentTimeMillis()-startTime);
}
}
@Override