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fast-bwa
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PE NOT working, yet

This commit is contained in:
Heng Li 2013-02-11 16:10:14 -05:00
parent 99907c98fb
commit dcb190069a
1 changed files with 12 additions and 3 deletions
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15
bwamem_pair.c
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@ -1,4 +1,5 @@
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include "kstring.h"
#include "bwamem.h"
@ -12,6 +13,11 @@
#define MAX_STDDEV 4.0
#define EXT_STDDEV 4.0
typedef kvec_t(uint64_t) vec64_t;
extern void ks_introsort_uint64_t(size_t n, uint64_t *a);
void bwa_hit2sam(kstring_t *str, const int8_t mat[25], int q, int r, int w, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, bwahit_t *p, int is_hard);
static int cal_sub(const mem_opt_t *opt, mem_alnreg_v *r)
{
int j;
@ -26,9 +32,6 @@ static int cal_sub(const mem_opt_t *opt, mem_alnreg_v *r)
return j < r->n? r->a[j].score : opt->min_seed_len * opt->a;
}
typedef kvec_t(uint64_t) vec64_t;
extern void ks_introsort_uint64_t(size_t n, uint64_t *a);
void mem_pestat(const mem_opt_t *opt, int64_t l_pac, int n, const mem_alnreg_v *regs, mem_pestat_t pes[4])
{
extern void ks_introsort_uint64_t(size_t n, uint64_t *a);
@ -116,6 +119,12 @@ void mem_pair(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, con
void mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], bseq1_t s[2], mem_alnreg_v a[2])
{
kstring_t str;
bwahit_t h[2];
str.l = str.m = 0; str.s = 0;
mem_pair(opt, bns, pac, pes, s, a, h);
bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, &s[0], &h[0], opt->is_hard);
s[0].sam = strdup(str.s); str.l = 0;
bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, &s[1], &h[1], opt->is_hard);
s[1].sam = str.s;
}