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Added option to write output to file

This commit is contained in:
José Manuel Abuín Mosquera 2015-03-24 10:35:46 +01:00 committed by John Marshall
parent ab3a92bc73
commit d28da05f36
1 changed files with 2 additions and 1 deletions
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3
fastmap.c
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@ -130,7 +130,7 @@ int main_mem(int argc, char *argv[])
aux.opt = opt = mem_opt_init();
memset(&opt0, 0, sizeof(mem_opt_t));
while ((c = getopt(argc, argv, "51paMCSPVYjk: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:X:H:")) >= 0) {
while ((c = getopt(argc, argv, "51paMCSPVYjk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:f:W:x:G:h:y:K:X:H:")) >= 0) {
if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
else if (c == '1') no_mt_io = 1;
else if (c == 'x') mode = optarg;
@ -158,6 +158,7 @@ int main_mem(int argc, char *argv[])
else if (c == 's') opt->split_width = atoi(optarg), opt0.split_width = 1;
else if (c == 'G') opt->max_chain_gap = atoi(optarg), opt0.max_chain_gap = 1;
else if (c == 'N') opt->max_chain_extend = atoi(optarg), opt0.max_chain_extend = 1;
else if (c == 'f') xreopen(optarg, "wb", stdout);
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 == 'C') aux.copy_comment = 1;