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move mem_fill_scmat() to bwa.{h,c}

This commit is contained in:
Heng Li 2013-03-05 09:38:12 -05:00
parent efd9769b07
commit 07921659cf
4 changed files with 14 additions and 13 deletions
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11
bwa.c
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@ -69,6 +69,17 @@ bseq1_t *bseq_read(int chunk_size, int *n_, void *ks1_, void *ks2_)
* CIGAR related *
*****************/
void bwa_fill_scmat(int a, int b, int8_t mat[25])
{
int i, j, k;
for (i = k = 0; i < 4; ++i) {
for (j = 0; j < 4; ++j)
mat[k++] = i == j? a : -b;
mat[k++] = 0; // ambiguous base
}
for (j = 0; j < 5; ++j) mat[k++] = 0;
}
// Generate CIGAR when the alignment end points are known
uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM)
{

1
bwa.h
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@ -30,6 +30,7 @@ extern "C" {
bseq1_t *bseq_read(int chunk_size, int *n_, void *ks1_, void *ks2_);
void bwa_fill_scmat(int a, int b, int8_t mat[25]);
uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM);
int bwa_fix_xref(const int8_t mat[25], int q, int r, int w, const bntseq_t *bns, const uint8_t *pac, uint8_t *query, int *qb, int *qe, int64_t *rb, int64_t *re);

13
bwamem.c
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@ -58,21 +58,10 @@ mem_opt_t *mem_opt_init()
o->chunk_size = 10000000;
o->n_threads = 1;
o->max_matesw = 100;
mem_fill_scmat(o->a, o->b, o->mat);
bwa_fill_scmat(o->a, o->b, o->mat);
return o;
}
void mem_fill_scmat(int a, int b, int8_t mat[25])
{
int i, j, k;
for (i = k = 0; i < 4; ++i) {
for (j = 0; j < 4; ++j)
mat[k++] = i == j? a : -b;
mat[k++] = 0; // ambiguous base
}
for (j = 0; j < 5; ++j) mat[k++] = 0;
}
/***************************
* SMEM iterator interface *
***************************/

2
fastmap.c
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@ -84,7 +84,7 @@ int main_mem(int argc, char *argv[])
return 1;
}
mem_fill_scmat(opt->a, opt->b, opt->mat);
bwa_fill_scmat(opt->a, opt->b, opt->mat);
if ((idx = bwa_idx_load(argv[optind], BWA_IDX_ALL)) == 0) return 1; // FIXME: memory leak
bwa_print_sam_hdr(idx->bns, rg_line);