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The BWA/C bindings were triggering the local aligner to repeatedly reload the 

ref genome.  Make sure the reference genome is cached.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1961 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-11-03 00:01:55 +00:00
parent 3a33401822
commit c63af32fc7
3 changed files with 19 additions and 9 deletions
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19
c/bwa/bwa_gateway.cpp
View File

@ -12,7 +12,13 @@ BWA::BWA(const char* ann_filename,
const char* reverse_bwt_filename,
const char* reverse_sa_filename)
{
// Load the bns (?) and reference
bns = bns_restore_core(ann_filename,amb_filename,pac_filename);
reference = new ubyte_t[bns->l_pac/4+1];
rewind(bns->fp_pac);
fread(reference, 1, bns->l_pac/4+1, bns->fp_pac);
// Load the BWTs (both directions) and suffix arrays (both directions)
bwts[0] = bwt_restore_bwt(forward_bwt_filename);
bwt_restore_sa(forward_sa_filename, bwts[0]);
bwts[1] = bwt_restore_bwt(reverse_bwt_filename);
@ -21,6 +27,8 @@ BWA::BWA(const char* ann_filename,
}
BWA::~BWA() {
delete[] reference;
bns_destroy(bns);
bwt_destroy(bwts[0]);
bwt_destroy(bwts[1]);
}
@ -105,8 +113,6 @@ void BWA::copy_bases_into_sequence(bwa_seq_t* sequence, const char* bases, const
}
void BWA::create_alignments(bwa_seq_t* sequence, Alignment*& alignments, unsigned& num_alignments) {
bool debug = false;
num_alignments = 0;
for(unsigned i = 0; i < (unsigned)sequence->n_aln; i++)
num_alignments += (sequence->aln + i)->l - (sequence->aln + i)->k + 1;
@ -138,14 +144,9 @@ void BWA::create_alignments(bwa_seq_t* sequence, Alignment*& alignments, unsigne
if(alignment_idx > 0)
seq_reverse(sequence->len, sequence->seq, 0);
// Calculate the local alignment.
// Calculate the local coordinate and local alignment.
bwa_cal_pac_pos_core(bwts[0],bwts[1],sequence,options.max_diff,options.fnr);
if(debug) {
printf("alignment_idx = %d, k = %d, l = %d, sa_idx = %d\n", alignment_idx, alignment_block->k, alignment_block->l, sa_idx);
printf("sequence->pos = %d\n",sequence->pos);
}
bwa_refine_gapped(bns, 1, sequence, 0, NULL);
bwa_refine_gapped(bns, 1, sequence, reference, NULL);
// Copy the local alignment data into the alignment object.
Alignment& alignment = *(alignments + alignment_idx);

1
c/bwa/bwa_gateway.h
View File

@ -12,6 +12,7 @@ class Alignment;
class BWA {
private:
bntseq_t *bns;
ubyte_t* reference;
bwt_t* bwts[2];
gap_opt_t options;

8
java/src/org/broadinstitute/sting/alignment/bwa/AlignmentValidationWalker.java
View File

@ -30,6 +30,11 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
*/
private int count = 0;
/**
* Max delta in mapping quality.
*/
private int maxMapQDelta = 0;
/**
* Create an aligner object. The aligner object will load and hold the BWT until close() is called.
*/
@ -77,6 +82,8 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
matches &= (alignment.getAlignmentStart() == read.getAlignmentStart());
matches &= (alignment.isNegativeStrand() == read.getReadNegativeStrandFlag());
matches &= (alignment.getCigar().equals(read.getCigar()));
int mapQDelta = Math.abs(alignment.getMappingQuality()-read.getMappingQuality());
maxMapQDelta = Math.max(mapQDelta,maxMapQDelta);
//matches &= (alignment.getMappingQuality() == read.getMappingQuality());
if(matches) break;
}
@ -133,6 +140,7 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
@Override
public void onTraversalDone(Integer result) {
aligner.close();
out.printf("Max mapping quality delta: %s%n", maxMapQDelta);
super.onTraversalDone(result);
}