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Added very primitive read fishing walker with lots of hard coding. Fixed 

bugs encountered when testing read fishing in Ecoli.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2496 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-01-04 00:54:57 +00:00
parent 7b702b086f
commit 29c129aced
3 changed files with 111 additions and 14 deletions
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45
java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.alignment.bwa;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
import org.broadinstitute.sting.alignment.reference.bwt.BWT;
import org.broadinstitute.sting.alignment.reference.bwt.BWTWriter;
@ -14,6 +15,7 @@ import java.io.IOException;
import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.util.StringUtil;
/**
* Support files for BWT.
@ -132,14 +134,18 @@ public class BWTFiles {
* @return A new object representing encoded representations of each sequence.
*/
public static BWTFiles createFromReferenceSequence(byte[] referenceSequence) {
byte[] normalizedReferenceSequence = new byte[referenceSequence.length];
System.arraycopy(referenceSequence,0,normalizedReferenceSequence,0,referenceSequence.length);
normalizeReferenceSequence(normalizedReferenceSequence);
File annFile,ambFile,pacFile,bwtFile,saFile,rpacFile,rbwtFile,rsaFile;
try {
// Write the ann and amb for this reference sequence.
annFile = File.createTempFile("bwt","ann");
ambFile = File.createTempFile("bwt","amb");
annFile = File.createTempFile("bwt",".ann");
ambFile = File.createTempFile("bwt",".amb");
SAMSequenceDictionary dictionary = new SAMSequenceDictionary();
dictionary.addSequence(new SAMSequenceRecord("autogenerated",referenceSequence.length));
dictionary.addSequence(new SAMSequenceRecord("autogenerated",normalizedReferenceSequence.length));
ANNWriter annWriter = new ANNWriter(annFile);
annWriter.write(dictionary);
@ -150,19 +156,18 @@ public class BWTFiles {
ambWriter.close();
// Write the encoded files for the forward version of this reference sequence.
pacFile = File.createTempFile("bwt","pac");
bwtFile = File.createTempFile("bwt","bwt");
saFile = File.createTempFile("bwt","sa");
pacFile = File.createTempFile("bwt",".pac");
bwtFile = File.createTempFile("bwt",".bwt");
saFile = File.createTempFile("bwt",".sa");
writeEncodedReferenceSequence(referenceSequence,pacFile,bwtFile,saFile);
writeEncodedReferenceSequence(normalizedReferenceSequence,pacFile,bwtFile,saFile);
// Write the encoded files for the reverse version of this reference sequence.
byte[] reverseReferenceSequence = new byte[referenceSequence.length];
System.arraycopy(referenceSequence,0,reverseReferenceSequence,0,referenceSequence.length);
byte[] reverseReferenceSequence = BaseUtils.reverse(normalizedReferenceSequence);
rpacFile = File.createTempFile("bwt","rpac");
rbwtFile = File.createTempFile("bwt","rbwt");
rsaFile = File.createTempFile("bwt","rsa");
rpacFile = File.createTempFile("bwt",".rpac");
rbwtFile = File.createTempFile("bwt",".rbwt");
rsaFile = File.createTempFile("bwt",".rsa");
writeEncodedReferenceSequence(reverseReferenceSequence,rpacFile,rbwtFile,rsaFile);
}
@ -207,5 +212,19 @@ public class BWTFiles {
SuffixArrayWriter suffixArrayWriter = new SuffixArrayWriter(suffixArrayFile);
suffixArrayWriter.write(suffixArray);
suffixArrayWriter.close();
}
}
/**
* Convert the given reference sequence into a form suitable for building into
* on-the-fly sequences.
* @param referenceSequence The reference sequence to normalize.
* @throws StingException if normalized sequence cannot be generated.
*/
private static void normalizeReferenceSequence(byte[] referenceSequence) {
StringUtil.toUpperCase(referenceSequence);
for(byte base: referenceSequence) {
if(base != 'A' && base != 'C' && base != 'G' && base != 'T')
throw new StingException(String.format("Base type %c is not supported when building references on-the-fly",(char)base));
}
}
}

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

@ -45,7 +45,7 @@ public class SuffixArrayWriter {
uintPackedOutputStream.write(1);
// Length of the suffix array.
uintPackedOutputStream.write(suffixArray.length()-1);
uintPackedOutputStream.write(suffixArray.sequence,1,suffixArray.sequence.length);
uintPackedOutputStream.write(suffixArray.sequence,1,suffixArray.sequence.length-1);
}
catch( IOException ex ) {
throw new StingException("Unable to read BWT from input stream.", ex);

78
java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java 100644
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@ -0,0 +1,78 @@
package org.broadinstitute.sting.oneoffprojects.walkers;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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.StingException;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceRecord;
import net.sf.picard.reference.ReferenceSequence;
import java.io.IOException;
/**
* A walker to experiment with fishing for reads in the GATK. Has very limited utility in its current state.
*
* @author mhanna
* @version 0.1
*/
public class TestReadFishingWalker extends ReadWalker<Integer,Long> {
/**
* An aligner for the small custom reference.
*/
private BWAAligner aligner;
@Override
public void initialize() {
ReferenceSequence initialBases;
try {
IndexedFastaSequenceFile reader = new IndexedFastaSequenceFile(getToolkit().getArguments().referenceFile);
SAMSequenceRecord firstSequence = reader.getSequenceDictionary().getSequences().get(0);
initialBases = reader.getSubsequenceAt(firstSequence.getSequenceName(),1,100);
}
catch(IOException ex) {
throw new StingException("Unable to load initial bases from reference sequence");
}
aligner = new BWACAligner(initialBases.getBases(),new BWAConfiguration());
}
@Override
public Integer map(char[] ref, SAMRecord read) {
Alignment bestAlignment = aligner.getBestAlignment(read.getReadBases());
System.out.println("bestAlignment = " + bestAlignment);
return 1;
}
/**
* Provide an initial value for reduce computations.
* @return Initial value of reduce.
*/
@Override
public Long reduceInit() {
return 0L;
}
/**
* Reduces a single map with the accumulator provided as the ReduceType.
* @param value result of the map.
* @param accum accumulator for the reduce.
* @return accumulator with result of the map taken into account.
*/
@Override
public Long reduce(Integer value, Long accum) {
return value + accum;
}
@Override
public void onTraversalDone(Long result) {
aligner.close();
super.onTraversalDone(result);
}
}