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Fixed epic memory leak. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1934 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-10-29 16:32:43 +00:00
parent 2b96b2e4e7
commit f04b80d7db
4 changed files with 58 additions and 43 deletions
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89
c/bwa/bwa_gateway.cpp
View File

@ -27,21 +27,22 @@ BWA::~BWA() {
void BWA::align(const char* bases, const unsigned read_length, Alignment*& alignments, unsigned& num_alignments)
{
bwa_seq_t sequence;
initialize_sequence(sequence);
bwa_seq_t* sequence = create_sequence();
copy_bases_into_sequence(sequence, bases, read_length, true);
// Calculate the suffix array interval for each sequence, storing the result in sequence.aln (and sequence.n_aln).
// This method will destroy the contents of seq and rseq.
bwa_cal_sa_reg_gap(0,bwts,1,&sequence,&options);
bwa_cal_sa_reg_gap(0,bwts,1,sequence,&options);
// Translate suffix array indices into exactly how many alignments have been found.
bwa_aln2seq(sequence.n_aln,sequence.aln,&sequence);
bwa_aln2seq(sequence->n_aln,sequence->aln,sequence);
// Calculate and refine the position for each alignment. This position may be inaccurate
// if the read contains indels, etc. Refinement requires the original sequences in the proper order.
copy_bases_into_sequence(sequence, bases, read_length, false);
create_alignments(sequence, alignments, num_alignments);
bwa_free_read_seq(1,sequence);
}
void BWA::load_default_options()
@ -64,44 +65,55 @@ void BWA::load_default_options()
options.trim_qual = 0;
}
void BWA::initialize_sequence(bwa_seq_t& sequence)
/**
* Create a sequence with a set of reasonable initial defaults.
* Will leave seq and rseq empty.
*/
bwa_seq_t* BWA::create_sequence()
{
sequence.tid = -1;
sequence.name = 0;
sequence.qual = 0;
bwa_seq_t* sequence = new bwa_seq_t;
sequence.seq = NULL;
sequence.rseq = NULL;
sequence->tid = -1;
sequence.cigar = 0;
sequence.n_cigar = NULL;
sequence->name = 0;
sequence->seq = NULL;
sequence->rseq = NULL;
sequence->qual = 0;
sequence->aln = 0;
sequence->md = 0;
sequence->cigar = NULL;
sequence->n_cigar = 0;
return sequence;
}
void BWA::copy_bases_into_sequence(bwa_seq_t& sequence, const char* bases, unsigned read_length, bool reverse)
void BWA::copy_bases_into_sequence(bwa_seq_t* sequence, const char* bases, unsigned read_length, bool reverse)
{
// seq, rseq will ultimately be freed by bwa_cal_sa_reg_gap
sequence.seq = new ubyte_t[read_length];
sequence.rseq = new ubyte_t[read_length];
for(unsigned i = 0; i < read_length; i++) sequence.seq[i] = nst_nt4_table[(unsigned)bases[i]];
memcpy(sequence.rseq,sequence.seq,read_length);
sequence->seq = new ubyte_t[read_length];
sequence->rseq = new ubyte_t[read_length];
for(unsigned i = 0; i < read_length; i++) sequence->seq[i] = nst_nt4_table[(unsigned)bases[i]];
memcpy(sequence->rseq,sequence->seq,read_length);
if(reverse) {
seq_reverse(read_length,sequence.seq,0);
seq_reverse(read_length,sequence.rseq,1);
seq_reverse(read_length,sequence->seq,0);
seq_reverse(read_length,sequence->rseq,1);
}
sequence.full_len = sequence.len = read_length;
sequence->full_len = sequence->len = read_length;
}
void BWA::create_alignments(bwa_seq_t& sequence, Alignment*& alignments, unsigned& num_alignments) {
void BWA::create_alignments(bwa_seq_t* sequence, Alignment*& alignments, unsigned& num_alignments) {
num_alignments = 0;
for(unsigned i = 0; i < (unsigned)sequence.n_aln; i++)
num_alignments += (sequence.aln + i)->l - (sequence.aln + i)->k + 1;
for(unsigned i = 0; i < (unsigned)sequence->n_aln; i++)
num_alignments += (sequence->aln + i)->l - (sequence->aln + i)->k + 1;
alignments = new Alignment[num_alignments];
unsigned alignment_idx = 0;
// backup existing alignment blocks.
bwt_aln1_t* alignment_blocks = sequence.aln;
int num_alignment_blocks = sequence.n_aln;
bwt_aln1_t* alignment_blocks = sequence->aln;
int num_alignment_blocks = sequence->n_aln;
for(unsigned alignment_block_idx = 0; alignment_block_idx < (unsigned)num_alignment_blocks; alignment_block_idx++) {
// Stub in a 'working' alignment block, so that only the desired alignment is local-aligned.
@ -111,27 +123,28 @@ void BWA::create_alignments(bwa_seq_t& sequence, Alignment*& alignments, unsigne
// Loop through all alignments, aligning each one individually.
for(unsigned sa_idx = alignment_block->k; sa_idx <= alignment_block->l; sa_idx++) {
working_alignment_block.k = working_alignment_block.l = sa_idx;
sequence.aln = &working_alignment_block;
sequence.n_aln = 1;
sequence->aln = &working_alignment_block;
sequence->n_aln = 1;
// Calculate the local alignment.
bwa_cal_pac_pos_core(bwts[0],bwts[1],&sequence,options.max_diff,options.fnr);
bwa_refine_gapped(bns, 1, &sequence, 0, NULL);
bwa_cal_pac_pos_core(bwts[0],bwts[1],sequence,options.max_diff,options.fnr);
bwa_refine_gapped(bns, 1, sequence, 0, NULL);
// Copy the local alignment data into the alignment object.
Alignment& alignment = *(alignments + alignment_idx);
alignment.type = sequence.type;
bns_coor_pac2real(bns, sequence.pos, pos_end(&sequence) - sequence.pos, &alignment.contig);
alignment.pos = sequence.pos - bns->anns[alignment.contig].offset + 1;
alignment.negative_strand = sequence.strand;
alignment.cigar = sequence.cigar;
alignment.n_cigar = sequence.n_cigar;
alignment.mapQ = sequence.mapQ;
alignment.type = sequence->type;
bns_coor_pac2real(bns, sequence->pos, pos_end(sequence) - sequence->pos, &alignment.contig);
alignment.pos = sequence->pos - bns->anns[alignment.contig].offset + 1;
alignment.negative_strand = sequence->strand;
alignment.cigar = sequence->cigar;
alignment.n_cigar = sequence->n_cigar;
alignment.mapQ = sequence->mapQ;
alignment_idx++;
}
}
sequence.aln = alignment_blocks;
sequence.n_aln = num_alignment_blocks;
// Restore original alignment blocks.
sequence->aln = alignment_blocks;
sequence->n_aln = num_alignment_blocks;
}

6
c/bwa/bwa_gateway.h
View File

@ -16,9 +16,9 @@ class BWA {
gap_opt_t options;
void load_default_options();
void initialize_sequence(bwa_seq_t& sequence);
void copy_bases_into_sequence(bwa_seq_t& sequence, const char* bases, const unsigned read_length, const bool reverse);
void create_alignments(bwa_seq_t& sequence, Alignment*& alignments, unsigned& num_alignments);
bwa_seq_t* create_sequence();
void copy_bases_into_sequence(bwa_seq_t* sequence, const char* bases, const unsigned read_length, const bool reverse);
void create_alignments(bwa_seq_t* sequence, Alignment*& alignments, unsigned& num_alignments);
public:
BWA(const char* ann_filename,

2
c/bwa/org_broadinstitute_sting_alignment_bwa_BWACAligner.cpp
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@ -67,7 +67,7 @@ JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_sting_alignment_bwa_BWACA
jbyte *read_bases = env->GetByteArrayElements(java_bases,JNI_FALSE);
Alignment* alignments = NULL;
unsigned num_alignments = 1;
unsigned num_alignments = 0;
bwa->align((const char*)read_bases,read_length,alignments,num_alignments);
jobjectArray java_alignments = env->NewObjectArray(num_alignments, env->FindClass("org/broadinstitute/sting/alignment/Alignment"), NULL);

4
java/src/org/broadinstitute/sting/alignment/bwa/BWACAligner.java
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@ -113,6 +113,7 @@ public class BWACAligner {
count++;
//if(count > 1) break;
Alignment[] alignments = thunk.align(read.getReadBases());
/*
System.out.printf("Read: %s: ", read.getReadName());
for(Alignment alignment: alignments)
System.out.printf("tig = %d; pos = %d, neg strand = %b, mapQ = %d, cigar = %s;",
@ -121,8 +122,9 @@ public class BWACAligner {
alignment.isNegativeStrand(),
alignment.getMappingQuality(),
alignment.getCigarString());
*/
if(count % 10000 == 0) System.out.printf("Processed %d reads.%n",count);
System.out.printf("%n");
//System.out.printf("%n");
}
thunk.close();