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Finishing off data transfer conduits for single alignment generator. 

Misc bug fixes elsewhere.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2101 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-11-20 15:21:59 +00:00
parent 2a5349d886
commit 38a030f2ba
6 changed files with 84 additions and 23 deletions
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16
c/bwa/bwa_gateway.cpp
View File

@ -56,12 +56,18 @@ void BWA::find_paths(const char* bases, const unsigned read_length, bwt_aln1_t*&
bwa_free_read_seq(1,sequence);
}
Alignment BWA::generate_single_alignment(const char* bases, const unsigned read_length) {
Alignment* BWA::generate_single_alignment(const char* bases, const unsigned read_length) {
bwa_seq_t* sequence = create_sequence(bases,read_length);
// Calculate paths.
bwa_cal_sa_reg_gap(0,bwts,1,sequence,&options);
// Check for no alignments found and return null.
if(sequence->n_aln == 0) {
bwa_free_read_seq(1,sequence);
return NULL;
}
// bwa_cal_sa_reg_gap destroys the bases / read length. Copy them back in.
copy_bases_into_sequence(sequence,bases,read_length);
@ -69,7 +75,8 @@ Alignment BWA::generate_single_alignment(const char* bases, const unsigned read_
bwa_aln2seq(sequence->n_aln,sequence->aln,sequence);
// Generate the best alignment from the sequence.
Alignment alignment = generate_final_alignment_from_sequence(sequence);
Alignment* alignment = new Alignment;
*alignment = generate_final_alignment_from_sequence(sequence);
bwa_free_read_seq(1,sequence);
@ -148,6 +155,7 @@ Alignment BWA::generate_final_alignment_from_sequence(bwa_seq_t* sequence) {
Alignment alignment;
// Populate basic path info
alignment.edit_distance = sequence->nm;
alignment.num_mismatches = sequence->n_mm;
alignment.num_gap_opens = sequence->n_gapo;
alignment.num_gap_extensions = sequence->n_gape;
@ -168,7 +176,9 @@ Alignment BWA::generate_final_alignment_from_sequence(bwa_seq_t* sequence) {
memcpy(alignment.cigar,sequence->cigar,sequence->n_cigar*sizeof(uint16_t));
}
alignment.n_cigar = sequence->n_cigar;
// MD tag with a better breakdown of differences in the cigar
alignment.md = strdup(sequence->md);
delete[] sequence->md;
sequence->md = NULL;

8
c/bwa/bwa_gateway.h
View File

@ -21,8 +21,12 @@ class Alignment {
uint8_t num_mismatches;
uint8_t num_gap_opens;
uint8_t num_gap_extensions;
uint16_t edit_distance;
uint32_t num_best;
uint32_t num_second_best;
char* md;
};
class BWA {
@ -57,8 +61,8 @@ class BWA {
void set_gap_extension_penalty(int penalty);
// Perform the alignment
Alignment generate_single_alignment(const char* bases,
const unsigned read_length);
Alignment* generate_single_alignment(const char* bases,
const unsigned read_length);
void find_paths(const char* bases,
const unsigned read_length,
bwt_aln1_t*& paths,

16
c/bwa/org_broadinstitute_sting_alignment_bwa_c_BWACAligner.cpp
View File

@ -252,8 +252,9 @@ JNIEXPORT jobject JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAlig
jbyte *read_bases = env->GetByteArrayElements(java_bases,JNI_FALSE);
if(read_bases == NULL) return NULL;
Alignment best_alignment = bwa->generate_single_alignment((const char*)read_bases,read_length);
jobject java_best_alignment = convert_to_java_alignment(env,read_bases,read_length,best_alignment);
Alignment* best_alignment = bwa->generate_single_alignment((const char*)read_bases,read_length);
jobject java_best_alignment = (best_alignment != NULL) ? convert_to_java_alignment(env,read_bases,read_length,*best_alignment) : NULL;
delete best_alignment;
env->ReleaseByteArrayElements(java_bases,read_bases,JNI_FALSE);
@ -291,12 +292,17 @@ static jobject convert_to_java_alignment(JNIEnv *env, const jbyte* read_bases, c
if(env->ExceptionCheck()) return NULL;
}
}
delete[] alignment.cigar;
jclass java_alignment_class = env->FindClass("org/broadinstitute/sting/alignment/Alignment");
if(java_alignment_class == NULL) return NULL;
jmethodID java_alignment_constructor = env->GetMethodID(java_alignment_class, "<init>", "(IIZI[C[IIIIII)V");
jmethodID java_alignment_constructor = env->GetMethodID(java_alignment_class, "<init>", "(IIZI[C[IILjava/lang/String;IIIII)V");
if(java_alignment_constructor == NULL) return NULL;
jstring java_md = env->NewStringUTF(alignment.md);
if(java_md == NULL) return NULL;
delete[] alignment.md;
jobject java_alignment = env->NewObject(java_alignment_class,
java_alignment_constructor,
@ -306,6 +312,8 @@ static jobject convert_to_java_alignment(JNIEnv *env, const jbyte* read_bases, c
alignment.mapping_quality,
java_cigar_operators,
java_cigar_lengths,
alignment.edit_distance,
java_md,
alignment.num_mismatches,
alignment.num_gap_opens,
alignment.num_gap_extensions,
@ -313,8 +321,6 @@ static jobject convert_to_java_alignment(JNIEnv *env, const jbyte* read_bases, c
alignment.num_second_best);
if(java_alignment == NULL) return NULL;
delete[] alignment.cigar;
env->DeleteLocalRef(java_alignment_class);
if(env->ExceptionCheck()) return NULL;

20
java/src/org/broadinstitute/sting/alignment/Alignment.java
View File

@ -19,6 +19,9 @@ public class Alignment {
protected char[] cigarOperators;
protected int[] cigarLengths;
protected int editDistance;
protected String mismatchingPositions;
protected int numMismatches;
protected int numGapOpens;
protected int numGapExtensions;
@ -49,6 +52,19 @@ public class Alignment {
*/
public int getMappingQuality() { return mappingQuality; }
/**
* Gets the edit distance; will eventually end up in the NM SAM tag
* if this alignment makes it that far.
* @return The edit distance.
*/
public int getEditDistance() { return editDistance; }
/**
* A string representation of which positions mismatch; contents of MD tag.
* @return String representation of mismatching positions.
*/
public String getMismatchingPositions() { return mismatchingPositions; }
/**
* Gets the number of mismatches in the read.
* @return Number of mismatches.
@ -129,6 +145,8 @@ public class Alignment {
int mappingQuality,
char[] cigarOperators,
int[] cigarLengths,
int editDistance,
String mismatchingPositions,
int numMismatches,
int numGapOpens,
int numGapExtensions,
@ -140,6 +158,8 @@ public class Alignment {
this.mappingQuality = mappingQuality;
this.cigarOperators = cigarOperators;
this.cigarLengths = cigarLengths;
this.editDistance = editDistance;
this.mismatchingPositions = mismatchingPositions;
this.numMismatches = numMismatches;
this.numGapOpens = numGapOpens;
this.numGapExtensions = numGapExtensions;

24
java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java
View File

@ -6,9 +6,8 @@ import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
import org.broadinstitute.sting.alignment.bwa.c.BWACConfiguration;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.*;
import net.sf.picard.reference.ReferenceSequenceFileFactory;
/**
* Align reads to the reference specified by BWTPrefix.
@ -37,6 +36,14 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
*/
private SAMFileWriter outputBam = null;
/** Must return true for reads that need to be processed. Reads, for which this method return false will
* be skipped by the engine and never passed to the walker.
*/
@Override
public boolean filter(char[] ref, SAMRecord read) {
return true;
}
/**
* Create an aligner object. The aligner object will load and hold the BWT until close() is called.
*/
@ -45,8 +52,17 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
BWACConfiguration configuration = new BWACConfiguration(prefix);
aligner = new BWACAligner(configuration);
// HACK: If the sequence dictionary in the existing header is null, stuff the contents of the current reference
// into it, so that the sequence has something to which to back-align.
SAMFileHeader header = getToolkit().getSAMFileHeader();
if(header.getSequenceDictionary().isEmpty()) {
SAMSequenceDictionary referenceDictionary =
ReferenceSequenceFileFactory.getReferenceSequenceFile(getToolkit().getArguments().referenceFile).getSequenceDictionary();
header.setSequenceDictionary(referenceDictionary);
}
if ( outputBamFile != null ) {
SAMFileHeader header = this.getToolkit().getSAMFileHeader();
// Stuff the header from the fasta into that of the sequence dictionary.
outputBam = Utils.createSAMFileWriterWithCompression(header, false, outputBamFile, bamCompression);
}
}

23
java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java
View File

@ -145,21 +145,26 @@ public class BWACAligner {
/**
* Creates a read directly from an alignment.
* @param unmappedRead Source of the unmapped read. Should have bases, quality scores, and flags.
* @param alignment The target alignment for this read.
* @param alignment The target alignment for this read. If alignment is null, assume the read is unmappe.d
* @return A mapped alignment.
*/
public SAMRecord convertAlignmentToRead(SAMRecord unmappedRead, Alignment alignment) {
SAMRecord read = null;
try {
read = (SAMRecord)unmappedRead.clone();
read.setReadUmappedFlag(false);
read.setAlignmentStart((int)alignment.getAlignmentStart());
read.setReadNegativeStrandFlag(alignment.isNegativeStrand());
read.setMappingQuality(alignment.getMappingQuality());
read.setCigar(alignment.getCigar());
if(alignment.isNegativeStrand()) {
read.setReadBases(BaseUtils.reverse(read.getReadBases()));
read.setBaseQualities(BaseUtils.reverse(read.getBaseQualities()));
if(alignment != null) {
read.setReadUmappedFlag(false);
read.setReferenceIndex(alignment.getContigIndex());
read.setAlignmentStart((int)alignment.getAlignmentStart());
read.setReadNegativeStrandFlag(alignment.isNegativeStrand());
read.setMappingQuality(alignment.getMappingQuality());
read.setCigar(alignment.getCigar());
if(alignment.isNegativeStrand()) {
read.setReadBases(BaseUtils.reverse(read.getReadBases()));
read.setBaseQualities(BaseUtils.reverse(read.getBaseQualities()));
}
read.setAttribute("NM",alignment.getEditDistance());
read.setAttribute("MD",alignment.getMismatchingPositions());
}
}
catch(CloneNotSupportedException ex) {