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do not use .64 suffix by default

This commit is contained in:
Heng Li 2012-03-29 12:31:01 -04:00
parent bdc953cad9
commit c875085b2b
1 changed files with 7 additions and 5 deletions
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12
bwtindex.c
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@ -42,11 +42,11 @@ void bwa_pac_rev_core(const char *fn, const char *fn_rev);
int bwa_index(int argc, char *argv[]) int bwa_index(int argc, char *argv[])
{ {
char *prefix = 0, *str, *str2, *str3; char *prefix = 0, *str, *str2, *str3;
int c, algo_type = 0, is_color = 0; int c, algo_type = 0, is_color = 0, is_64 = 0;
clock_t t; clock_t t;
int64_t l_pac; int64_t l_pac;
while ((c = getopt(argc, argv, "ca:p:")) >= 0) { while ((c = getopt(argc, argv, "6ca:p:")) >= 0) {
switch (c) { switch (c) {
case 'a': // if -a is not set, algo_type will be determined later case 'a': // if -a is not set, algo_type will be determined later
if (strcmp(optarg, "div") == 0) algo_type = 1; if (strcmp(optarg, "div") == 0) algo_type = 1;
@ -56,15 +56,17 @@ int bwa_index(int argc, char *argv[])
break; break;
case 'p': prefix = strdup(optarg); break; case 'p': prefix = strdup(optarg); break;
case 'c': is_color = 1; break; case 'c': is_color = 1; break;
case '6': is_64 = 1; break;
default: return 1; default: return 1;
} }
} }
if (optind + 1 > argc) { if (optind + 1 > argc) {
fprintf(stderr, "\n"); fprintf(stderr, "\n");
fprintf(stderr, "Usage: bwa index [-a bwtsw|div|is] [-c] <in.fasta>\n\n"); fprintf(stderr, "Usage: bwa index [-a bwtsw|is] [-c] <in.fasta>\n\n");
fprintf(stderr, "Options: -a STR BWT construction algorithm: bwtsw or is [is]\n"); fprintf(stderr, "Options: -a STR BWT construction algorithm: bwtsw or is [auto]\n");
fprintf(stderr, " -p STR prefix of the index [same as fasta name]\n"); fprintf(stderr, " -p STR prefix of the index [same as fasta name]\n");
fprintf(stderr, " -6 index files named as <in.fasta>.64.* instead of <in.fasta>.* \n");
// fprintf(stderr, " -c build color-space index\n"); // fprintf(stderr, " -c build color-space index\n");
fprintf(stderr, "\n"); fprintf(stderr, "\n");
fprintf(stderr, "Warning: `-a bwtsw' does not work for short genomes, while `-a is' and\n"); fprintf(stderr, "Warning: `-a bwtsw' does not work for short genomes, while `-a is' and\n");
@ -75,7 +77,7 @@ int bwa_index(int argc, char *argv[])
if (prefix == 0) { if (prefix == 0) {
prefix = malloc(strlen(argv[optind]) + 4); prefix = malloc(strlen(argv[optind]) + 4);
strcpy(prefix, argv[optind]); strcpy(prefix, argv[optind]);
strcat(prefix, ".64"); if (is_64) strcat(prefix, ".64");
} }
str = (char*)calloc(strlen(prefix) + 10, 1); str = (char*)calloc(strlen(prefix) + 10, 1);
str2 = (char*)calloc(strlen(prefix) + 10, 1); str2 = (char*)calloc(strlen(prefix) + 10, 1);