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r830: optionally fixed chunk size

This commit is contained in:
Heng Li 2014-09-15 23:42:24 -04:00
parent 624687b072
commit 4b6eeb34c8
3 changed files with 6 additions and 6 deletions
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2
bwamem.c
View File

@ -1153,8 +1153,6 @@ void mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bn
double ctime, rtime; double ctime, rtime;
int i; int i;
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;
w.regs = malloc(n * sizeof(mem_alnreg_v)); w.regs = malloc(n * sizeof(mem_alnreg_v));

8
fastmap.c
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@ -39,6 +39,7 @@ int main_mem(int argc, char *argv[])
{ {
mem_opt_t *opt, opt0; mem_opt_t *opt, opt0;
int fd, fd2, i, c, n, copy_comment = 0; int fd, fd2, i, c, n, copy_comment = 0;
int fixed_chunk_size = -1, actual_chunk_size;
gzFile fp, fp2 = 0; gzFile fp, fp2 = 0;
kseq_t *ks, *ks2 = 0; kseq_t *ks, *ks2 = 0;
bseq1_t *seqs; bseq1_t *seqs;
@ -54,7 +55,7 @@ int main_mem(int argc, char *argv[])
opt = mem_opt_init(); opt = mem_opt_init();
memset(&opt0, 0, sizeof(mem_opt_t)); memset(&opt0, 0, sizeof(mem_opt_t));
while ((c = getopt(argc, argv, "epaFMCSPHVYk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:y:")) >= 0) { while ((c = getopt(argc, argv, "epaFMCSPHVYk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:y:K:")) >= 0) {
if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1; if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
else if (c == 'x') mode = optarg; else if (c == 'x') mode = optarg;
else if (c == 'w') opt->w = atoi(optarg), opt0.w = 1; else if (c == 'w') opt->w = atoi(optarg), opt0.w = 1;
@ -85,6 +86,7 @@ int main_mem(int argc, char *argv[])
else if (c == 'W') opt->min_chain_weight = atoi(optarg), opt0.min_chain_weight = 1; else if (c == 'W') opt->min_chain_weight = atoi(optarg), opt0.min_chain_weight = 1;
else if (c == 'y') opt->max_mem_intv = atol(optarg), opt0.max_mem_intv = 1; else if (c == 'y') opt->max_mem_intv = atol(optarg), opt0.max_mem_intv = 1;
else if (c == 'C') copy_comment = 1; else if (c == 'C') copy_comment = 1;
else if (c == 'K') fixed_chunk_size = atoi(optarg);
else if (c == 'Q') { else if (c == 'Q') {
opt0.mapQ_coef_len = 1; opt0.mapQ_coef_len = 1;
opt->mapQ_coef_len = atoi(optarg); opt->mapQ_coef_len = atoi(optarg);
@ -205,7 +207,6 @@ int main_mem(int argc, char *argv[])
return 1; // FIXME memory leak return 1; // FIXME memory leak
} }
} else update_a(opt, &opt0); } else update_a(opt, &opt0);
// if (opt->T < opt->min_HSP_score) opt->T = opt->min_HSP_score; // TODO: tie ->T to MEM_HSP_COEF
bwa_fill_scmat(opt->a, opt->b, opt->mat); bwa_fill_scmat(opt->a, opt->b, opt->mat);
if ((idx = bwa_idx_load(argv[optind], BWA_IDX_ALL)) == 0) return 1; // FIXME: memory leak if ((idx = bwa_idx_load(argv[optind], BWA_IDX_ALL)) == 0) return 1; // FIXME: memory leak
@ -234,7 +235,8 @@ int main_mem(int argc, char *argv[])
} }
if (!(opt->flag & MEM_F_ALN_REG)) if (!(opt->flag & MEM_F_ALN_REG))
bwa_print_sam_hdr(idx->bns, rg_line); bwa_print_sam_hdr(idx->bns, rg_line);
while ((seqs = bseq_read(opt->chunk_size * opt->n_threads, &n, ks, ks2)) != 0) { actual_chunk_size = fixed_chunk_size > 0? fixed_chunk_size : opt->chunk_size * opt->n_threads;
while ((seqs = bseq_read(actual_chunk_size, &n, ks, ks2)) != 0) {
int64_t size = 0; int64_t size = 0;
if ((opt->flag & MEM_F_PE) && (n&1) == 1) { if ((opt->flag & MEM_F_PE) && (n&1) == 1) {
if (bwa_verbose >= 2) if (bwa_verbose >= 2)

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.10-r829-dirty" #define PACKAGE_VERSION "0.7.10-r830-dirty"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);