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code backup

This commit is contained in:
Heng Li 2014-09-05 13:20:52 -04:00
parent e4ad616d43
commit 1934f0cf24
1 changed files with 8 additions and 7 deletions
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15
bwamem.c
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@ -1077,7 +1077,7 @@ typedef struct {
const mem_pestat_t *pes; const mem_pestat_t *pes;
smem_aux_t **aux; smem_aux_t **aux;
bseq1_t *seqs; bseq1_t *seqs;
mem_alnreg_v *regs; mem_alnreg_v *regs, *regs_alt;
int64_t n_processed; int64_t n_processed;
} worker_t; } worker_t;
@ -1120,16 +1120,17 @@ void mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bn
{ {
extern void kt_for(int n_threads, void (*func)(void*,int,int), void *data, int n); extern void kt_for(int n_threads, void (*func)(void*,int,int), void *data, int n);
worker_t w; worker_t w;
mem_alnreg_v *regs;
mem_pestat_t pes[4]; mem_pestat_t pes[4];
double ctime, rtime; double ctime, rtime;
int i; int i, has_alt = 0;
for (i = 0; i < bns->n_seqs; ++i)
if (bns->anns[i].is_alt) has_alt = 1;
ctime = cputime(); rtime = realtime(); ctime = cputime(); rtime = realtime();
global_bns = bns; global_bns = bns;
regs = malloc(n * sizeof(mem_alnreg_v)); w.regs = malloc(n * sizeof(mem_alnreg_v));
w.opt = opt; w.bwt = bwt; w.bns = bns; w.pac = pac; w.opt = opt; w.bwt = bwt; w.bns = bns; w.pac = pac;
w.seqs = seqs; w.regs = regs; w.n_processed = n_processed; w.seqs = seqs; w.n_processed = n_processed;
w.pes = &pes[0]; w.pes = &pes[0];
w.aux = malloc(opt->n_threads * sizeof(smem_aux_t)); w.aux = malloc(opt->n_threads * sizeof(smem_aux_t));
for (i = 0; i < opt->n_threads; ++i) for (i = 0; i < opt->n_threads; ++i)
@ -1140,10 +1141,10 @@ void mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bn
free(w.aux); free(w.aux);
if (opt->flag&MEM_F_PE) { // infer insert sizes if not provided if (opt->flag&MEM_F_PE) { // infer insert sizes if not provided
if (pes0) memcpy(pes, pes0, 4 * sizeof(mem_pestat_t)); // if pes0 != NULL, set the insert-size distribution as pes0 if (pes0) memcpy(pes, pes0, 4 * sizeof(mem_pestat_t)); // if pes0 != NULL, set the insert-size distribution as pes0
else mem_pestat(opt, bns->l_pac, n, regs, pes); // otherwise, infer the insert size distribution from data else mem_pestat(opt, bns->l_pac, n, w.regs, pes); // otherwise, infer the insert size distribution from data
} }
kt_for(opt->n_threads, worker2, &w, (opt->flag&MEM_F_PE)? n>>1 : n); // generate alignment kt_for(opt->n_threads, worker2, &w, (opt->flag&MEM_F_PE)? n>>1 : n); // generate alignment
free(regs); free(w.regs);
if (bwa_verbose >= 3) if (bwa_verbose >= 3)
fprintf(stderr, "[M::%s] Processed %d reads in %.3f CPU sec, %.3f real sec\n", __func__, n, cputime() - ctime, realtime() - rtime); fprintf(stderr, "[M::%s] Processed %d reads in %.3f CPU sec, %.3f real sec\n", __func__, n, cputime() - ctime, realtime() - rtime);
} }