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replace aln_global in bwase.c

This commit is contained in:
Heng Li 2013-03-05 10:38:47 -05:00
parent e6c262594f
commit bb37e14d02
1 changed files with 10 additions and 7 deletions
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17
bwase.c
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@ -11,6 +11,7 @@
#include "utils.h"
#include "kstring.h"
#include "bwa.h"
#include "ksw.h"
int g_log_n[256];
@ -164,12 +165,13 @@ bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int l
int ext, int *n_cigar, int is_end_correct)
{
bwa_cigar_t *cigar = 0;
uint32_t *cigar32 = 0;
ubyte_t *ref_seq;
int l = 0, path_len, ref_len;
AlnParam ap = aln_param_bwa;
path_t *path;
int l = 0, ref_len;
int64_t k, __pos = *_pos;
int8_t mat[25];
bwa_fill_scmat(1, 3, mat);
ref_len = len + abs(ext);
if (ext > 0) {
ref_seq = (ubyte_t*)calloc(ref_len, 1);
@ -181,10 +183,11 @@ bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int l
for (l = 0, k = x - ref_len > 0? x - ref_len : 0; k < x && k < l_pac; ++k)
ref_seq[l++] = pacseq[k>>2] >> ((~k&3)<<1) & 3;
}
path = (path_t*)calloc(l+len, sizeof(path_t));
aln_global_core(ref_seq, l, (ubyte_t*)seq, len, &ap, path, &path_len);
cigar = bwa_aln_path2cigar(path, path_len, n_cigar);
ksw_global(len, seq, l, ref_seq, 5, mat, 5, 1, 50, n_cigar, &cigar32);
cigar = (bwa_cigar_t*)cigar32;
for (k = 0; k < *n_cigar; ++k)
cigar[k] = __cigar_create((cigar32[k]&0xf), (cigar32[k]>>4));
if (ext < 0 && is_end_correct) { // fix coordinate for reads mapped to the forward strand
for (l = k = 0; k < *n_cigar; ++k) {
@ -206,7 +209,7 @@ bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int l
if (__cigar_op(cigar[0]) == FROM_I) cigar[0] = __cigar_create(3, (__cigar_len(cigar[0])));
*_pos = (bwtint_t)__pos;
free(ref_seq); free(path);
free(ref_seq);
return cigar;
}