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code backup

This commit is contained in:
Heng Li 2013-02-07 13:29:01 -05:00
parent 5dc398cdef
commit bfeb37c4de
2 changed files with 44 additions and 2 deletions
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44
bwamem.c
View File

@ -2,8 +2,10 @@
#include <string.h>
#include <stdio.h>
#include <assert.h>
#ifdef HAVE_PTHREAD
#include <pthread.h>
#endif
#include "bwamem.h"
#include "kvec.h"
#include "bntseq.h"
#include "ksw.h"
#include "ksort.h"
@ -422,8 +424,48 @@ static void process_seq1(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t
{
}
typedef struct {
int start, step, n;
const mem_opt_t *opt;
const bwt_t *bwt;
const bntseq_t *bns;
const uint8_t *pac;
bseq1_t *seqs;
} worker1_t;
static void *worker1(void *data)
{
worker1_t *w = (worker1_t*)data;
int i;
for (i = w->start; i < w->n; i += w->step)
process_seq1(w->opt, w->bwt, w->bns, w->pac, &w->seqs[i]);
return 0;
}
int mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int n, bseq1_t *seqs)
{
int i;
worker1_t *w1;
w1 = calloc(opt->n_threads, sizeof(worker1_t));
for (i = 0; i < opt->n_threads; ++i) {
worker1_t *w = &w1[i];
w->start = i; w->step = opt->n_threads; w->n = n;
w->opt = opt; w->bwt = bwt; w->bns = bns; w->pac = pac;
w->seqs = seqs;
}
#ifdef HAVE_PTHREAD
if (opt->n_threads == 1) {
worker1(w1);
} else {
pthread_t *tid;
tid = (pthread_t*)calloc(opt->n_threads, sizeof(pthread_t));
for (i = 0; i < opt->n_threads; ++i) pthread_create(&tid[i], 0, worker1, &w1[i]);
for (i = 0; i < opt->n_threads; ++i) pthread_join(tid[i], 0);
free(tid);
}
#else
worker1(w1);
#endif
free(w1);
return 0;
}

2
bwamem.h
View File

@ -34,7 +34,7 @@ typedef struct {
int score, qb, qe, sub;
} mem_alnreg_t;
typedef kvec_t(mem_chain_t) mem_chain_v;
typedef kvec_t(mem_chain_t) mem_chain_v;
typedef kvec_t(mem_alnreg_t) mem_alnreg_v;
#ifdef __cplusplus