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r437: print timing for each batch of reads

This commit is contained in:
Heng Li 2014-02-19 10:54:26 -05:00
parent bdd14d2946
commit 52391a9855
2 changed files with 5 additions and 1 deletions
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4
bwamem.c
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@ -1024,7 +1024,9 @@ void mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bn
worker_t w; worker_t w;
mem_alnreg_v *regs; mem_alnreg_v *regs;
mem_pestat_t pes[4]; mem_pestat_t pes[4];
double ctime, rtime;
ctime = cputime(); rtime = realtime();
regs = malloc(n * sizeof(mem_alnreg_v)); 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.regs = regs; w.n_processed = n_processed;
@ -1036,4 +1038,6 @@ void mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bn
} }
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(regs);
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);
} }

2
main.c
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@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.6a+dev-r436" #define PACKAGE_VERSION "0.7.6a+dev-r437"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);