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controllable scoring matrix

This commit is contained in:
Heng Li 2013-02-25 11:24:21 -05:00
parent 5ead86acd3
commit 5092211d75
1 changed files with 9 additions and 1 deletions
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10
fastmap.c
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@ -26,8 +26,12 @@ int main_mem(int argc, char *argv[])
void *ko = 0, *ko2 = 0; void *ko = 0, *ko2 = 0;
opt = mem_opt_init(); opt = mem_opt_init();
while ((c = getopt(argc, argv, "paMCPHk:c:v:s:r:t:R:")) >= 0) { while ((c = getopt(argc, argv, "paMCPHk:c:v:s:r:t:R:A:B:O:E:")) >= 0) {
if (c == 'k') opt->min_seed_len = atoi(optarg); if (c == 'k') opt->min_seed_len = atoi(optarg);
else if (c == 'A') opt->a = atoi(optarg);
else if (c == 'B') opt->b = atoi(optarg);
else if (c == 'O') opt->q = atoi(optarg);
else if (c == 'E') opt->r = atoi(optarg);
else if (c == 't') opt->n_threads = atoi(optarg), opt->n_threads = opt->n_threads > 1? opt->n_threads : 1; else if (c == 't') opt->n_threads = atoi(optarg), opt->n_threads = opt->n_threads > 1? opt->n_threads : 1;
else if (c == 'P') opt->flag |= MEM_F_NOPAIRING; else if (c == 'P') opt->flag |= MEM_F_NOPAIRING;
else if (c == 'H') opt->flag |= MEM_F_HARDCLIP; else if (c == 'H') opt->flag |= MEM_F_HARDCLIP;
@ -52,6 +56,10 @@ int main_mem(int argc, char *argv[])
fprintf(stderr, " -s INT look for internal seeds inside a seed with less than INT occ [%d]\n", opt->split_width); fprintf(stderr, " -s INT look for internal seeds inside a seed with less than INT occ [%d]\n", opt->split_width);
fprintf(stderr, " -c INT skip seeds with more than INT occurrences [%d]\n", opt->max_occ); fprintf(stderr, " -c INT skip seeds with more than INT occurrences [%d]\n", opt->max_occ);
fprintf(stderr, " -P skip pairing; perform mate SW only\n"); fprintf(stderr, " -P skip pairing; perform mate SW only\n");
fprintf(stderr, " -A INT score for a sequence match [%d]\n", opt->a);
fprintf(stderr, " -B INT penalty for a mismatch [%d]\n", opt->b);
fprintf(stderr, " -O INT gap open penalty [%d]\n", opt->q);
fprintf(stderr, " -E INT gap extension penalty; a gap of size k cost {-O} + {-E}*k [%d]\n", opt->r);
fprintf(stderr, "\nInput/output options:\n\n"); fprintf(stderr, "\nInput/output options:\n\n");
fprintf(stderr, " -p first query file consists of interleaved paired-end sequences\n"); fprintf(stderr, " -p first query file consists of interleaved paired-end sequences\n");
fprintf(stderr, " -R STR read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n"); fprintf(stderr, " -R STR read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n");