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main.c
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main.c
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#include <stdio.h>
#include <stdlib.h>
#include "mppriv.h"
#include "ketopt.h"
static ko_longopt_t long_options[] = {
{ "gff", ko_no_argument, 301 },
{ "xdrop", ko_required_argument, 302 },
{ "outn", ko_required_argument, 303 },
{ "gff-only", ko_no_argument, 304 },
{ "gff-delim", ko_required_argument, 305 },
{ "J2", ko_required_argument, 306 },
{ "gtf", ko_no_argument, 307 },
{ "outs", ko_required_argument, 308 },
{ "max-skip", ko_required_argument, 309 },
{ "no-pre-chain", ko_no_argument, 310 },
{ "aln", ko_no_argument, 311 },
{ "max-intron-out", ko_required_argument, 312 },
{ "outc", ko_required_argument, 313 },
{ "ie-coef", ko_required_argument, 314 },
{ "trans", ko_no_argument, 315 },
{ "no-cs", ko_no_argument, 316 },
{ "version", ko_no_argument, 401 },
{ "no-kalloc", ko_no_argument, 501 },
{ "dbg-qname", ko_no_argument, 502 },
{ "dbg-no-refine", ko_no_argument, 503 },
{ "dbg-aflt", ko_no_argument, 504 },
{ "dbg-anchor", ko_no_argument, 505 },
{ "dbg-chain", ko_no_argument, 506 },
{ 0, 0, 0 }
};
static inline int64_t mp_parse_num2(const char *str, char **q)
{
double x;
char *p;
x = strtod(str, &p);
if (*p == 'G' || *p == 'g') x *= 1e9, ++p;
else if (*p == 'M' || *p == 'm') x *= 1e6, ++p;
else if (*p == 'K' || *p == 'k') x *= 1e3, ++p;
if (q) *q = p;
return (int64_t)(x + .499);
}
static inline int64_t mp_parse_num(const char *str)
{
return mp_parse_num2(str, 0);
}
static void print_usage(FILE *fp, const mp_idxopt_t *io, const mp_mapopt_t *mo, int n_threads)
{
fprintf(fp, "Usage: miniprot [options] <ref.fa> <query.faa> [...]\n");
fprintf(fp, "Options:\n");
fprintf(fp, " Indexing:\n");
fprintf(fp, " -k INT k-mer size [%d]\n", io->kmer);
fprintf(fp, " -M INT modimisers bit (sample rate = 1/2**M) [%d]\n", io->mod_bit);
fprintf(fp, " -L INT min ORF length to index [%d]\n", io->min_aa_len);
fprintf(fp, " -T INT NCBI translation table (1 through 33) [%d]\n", io->trans_code);
fprintf(fp, " -b INT bits per block [%d]\n", io->bbit);
fprintf(fp, " -d FILE save index to FILE []\n");
fprintf(fp, " Mapping:\n");
fprintf(fp, " -S no splicing (applying -G1k -J1k -e1k)\n");
fprintf(fp, " -c NUM max k-mer occurrence [%d]\n", mo->max_occ);
fprintf(fp, " -G NUM max intron size; override -I [200k]\n");
fprintf(fp, " -I set max intron size to 3.6*sqrt(refLen)\n");
fprintf(fp, " -w FLOAT weight of log gap penalty [%g]\n", mo->chn_coef_log);
fprintf(fp, " -n NUM minimum number of syncmers in a chain [%d]\n", mo->min_chn_cnt);
fprintf(fp, " -m NUM min chaining score [%d]\n", mo->min_chn_sc);
fprintf(fp, " -l INT k-mer size for the second round of chaining [%d]\n", mo->kmer2);
fprintf(fp, " -e NUM max extension for 2nd round of chaining and alignment [%d]\n", mo->max_ext);
fprintf(fp, " -p FLOAT min secondary-to-primary score ratio [%g]\n", mo->pri_ratio);
fprintf(fp, " -N NUM consider at most INT secondary alignments [%d]\n", mo->best_n);
fprintf(fp, " Alignment:\n");
// fprintf(fp, " -A no alignment\n");
fprintf(fp, " -O INT gap open penalty [%d]\n", mo->go);
fprintf(fp, " -E INT gap extension (a k-long gap costs O+k*E) [%d]\n", mo->ge);
fprintf(fp, " -J INT intron open penalty [%d]\n", mo->io);
fprintf(fp, " -F INT penalty for frameshifts or in-frame stop codons [%d]\n", mo->fs);
fprintf(fp, " -C FLOAT weight of splice penalty; 0 to ignore splice signals [%g]\n", mo->sp_scale);
fprintf(fp, " -B INT bonus score for alignment reaching query ends [%d]\n", mo->end_bonus);
fprintf(fp, " -j INT splice model: 2=mammal, 1=general, 0=none (see manual) [%d]\n", mo->sp_model);
fprintf(fp, " Input/output:\n");
fprintf(fp, " -t INT number of threads [%d]\n", n_threads);
fprintf(fp, " --gff output in the GFF3 format\n");
fprintf(fp, " --gtf basic GTF output without detailed alignment\n");
fprintf(fp, " --aln output residue alignment\n");
fprintf(fp, " --trans output translated protein sequences (skipping frameshift)\n");
fprintf(fp, " -P STR prefix for IDs in GFF3 [%s]\n", mo->gff_prefix);
fprintf(fp, " -u print unmapped query proteins in PAF\n");
fprintf(fp, " --outn=NUM output up to min{NUM,-N} alignments per query [%d]\n", mo->out_n);
fprintf(fp, " --outs=FLOAT output if score at least FLOAT*bestScore [%g]\n", mo->out_sim);
fprintf(fp, " --outc=FLOAT output if at least FLOAT fraction of query is aligned [%g]\n", mo->out_cov);
fprintf(fp, " -K NUM query batch size [2M]\n");
}
int main(int argc, char *argv[])
{
int32_t c, i, set_I = 0, set_G = 0, n_threads = 4;
ketopt_t o = KETOPT_INIT;
mp_mapopt_t mo;
mp_idxopt_t io;
mp_idx_t *mi;
char *fn_idx = 0;
mp_start();
mp_mapopt_init(&mo);
mp_idxopt_init(&io);
while ((c = ketopt(&o, argc, argv, 1, "k:M:L:s:l:b:T:t:d:c:n:m:K:p:N:SAO:E:J:C:F:G:e:uB:P:w:j:g:I", long_options)) >= 0) {
if (c == 'k') io.kmer = atoi(o.arg);
else if (c == 'M') io.mod_bit = atoi(o.arg);
else if (c == 'L') io.min_aa_len = atoi(o.arg);
else if (c == 'b') io.bbit = atoi(o.arg);
else if (c == 'T') io.trans_code = atoi(o.arg);
else if (c == 'd') fn_idx = o.arg;
else if (c == 't') n_threads = atoi(o.arg);
else if (c == 'l') mo.kmer2 = atoi(o.arg);
else if (c == 'c') mo.max_occ = mp_parse_num(o.arg);
else if (c == 'G') mo.bw = mo.max_intron = mp_parse_num(o.arg), set_G = 1;
else if (c == 'I') set_I = 1;
else if (c == 'n') mo.min_chn_cnt = mp_parse_num(o.arg);
else if (c == 'm') mo.min_chn_sc = mp_parse_num(o.arg);
else if (c == 'K') mo.mini_batch_size = mp_parse_num(o.arg);
else if (c == 'p') mo.pri_ratio = atof(o.arg);
else if (c == 'N') mo.best_n = mp_parse_num(o.arg);
else if (c == 'S') mo.flag |= MP_F_NO_SPLICE, mo.bw = mo.max_intron = mo.max_ext = 1000, mo.io = mo.io_end = 10000, set_G = 1;
else if (c == 'A') mo.flag |= MP_F_NO_ALIGN;
else if (c == 'O') mo.go = atoi(o.arg);
else if (c == 'E') mo.ge = atoi(o.arg);
else if (c == 'J') mo.io = atoi(o.arg);
else if (c == 'C') mo.sp_scale = atof(o.arg);
else if (c == 'F') mp_mapopt_set_fs(&mo, atoi(o.arg));
else if (c == 'B') mo.end_bonus = atoi(o.arg);
else if (c == 'e') mo.max_ext = mp_parse_num(o.arg);
else if (c == 'P') mo.gff_prefix = o.arg;
else if (c == 'u') mo.flag |= MP_F_SHOW_UNMAP;
else if (c == 'w') mo.chn_coef_log = atof(o.arg);
else if (c == 'j') mo.sp_model = atoi(o.arg);
else if (c == 'g') mo.max_gap = mp_parse_num(o.arg);
else if (c == 301) mo.flag |= MP_F_GFF; // --gff
else if (c == 302) mo.xdrop = atoi(o.arg); // --xdrop
else if (c == 303) mo.out_n = mp_parse_num(o.arg); // --outn
else if (c == 308) mo.out_sim = atof(o.arg); // --outs
else if (c == 304) mo.flag |= MP_F_GFF | MP_F_NO_PAF; // --gff-only
else if (c == 305) mo.gff_delim = o.arg[0]; // --gff-delim
else if (c == 306) mo.io_end = atoi(o.arg); // --J2
else if (c == 307) mo.flag |= MP_F_GTF; // --gtf
else if (c == 309) mo.max_chn_max_skip = mp_parse_num(o.arg); // --max-skip
else if (c == 310) mo.flag |= MP_F_NO_PRE_CHAIN; // --no-pre-chain
else if (c == 311) mo.flag |= MP_F_SHOW_RESIDUE; // --aln
else if (c == 312) mo.max_intron_flank = (mp_parse_num(o.arg) + 1) / 2; // --max-intron-out
else if (c == 313) mo.out_cov = atof(o.arg); // --outc
else if (c == 314) mo.ie_coef = atof(o.arg); // --ie-coef
else if (c == 315) mo.flag |= MP_F_SHOW_TRANS; // --trans
else if (c == 316) mo.flag |= MP_F_NO_CS; // --no-cs
else if (c == 501) mp_dbg_flag |= MP_DBG_NO_KALLOC; // --no-kalloc
else if (c == 502) mp_dbg_flag |= MP_DBG_QNAME; // --dbg-qname
else if (c == 503) mp_dbg_flag |= MP_DBG_NO_REFINE; // --dbg-no-refine
else if (c == 504) mp_dbg_flag |= MP_DBG_MORE_DP; // --dbg-aflt
else if (c == 505) mp_dbg_flag |= MP_DBG_ANCHOR; // --dbg-anchor
else if (c == 506) mp_dbg_flag |= MP_DBG_CHAIN; // --dbg-chain
else if (c == 's') {
fprintf(stderr, "Option '-s' is deprecated.\n");
} else if (c == 401) {
printf("%s\n", MP_VERSION);
return 0;
} else {
fprintf(stderr, "[WARNING]\033[1;31m unrecognized option: %s\033[0m\n", argv[o.i-1]);
}
}
if (mp_mapopt_check(&mo) < 0) return 1;
if (argc - o.ind == 0 || (argc - o.ind == 1 && fn_idx == 0)) {
print_usage(stderr, &io, &mo, n_threads);
return 1;
}
if (ns_make_tables(io.trans_code) < 0) {
if (mp_verbose >= 1)
fprintf(stderr, "[ERROR]\033[1;31m failed to find translation table %d\033[0m\n", io.trans_code);
return 1;
}
mi = mp_idx_load(argv[o.ind], &io, n_threads);
if (mi == 0) {
if (mp_verbose >= 1)
fprintf(stderr, "[ERROR]\033[1;31m failed to open/build the index\033[0m\n");
return 1;
}
if (set_I && !set_G) mp_mapopt_set_max_intron(&mo, mi->nt->l_seq);
if (mp_verbose >= 3) mp_idx_print_stat(mi, mo.max_occ);
if (fn_idx != 0) mp_idx_dump(fn_idx, mi);
for (i = o.ind + 1; i < argc; ++i) {
int32_t res = mp_map_file(mi, argv[i], &mo, n_threads);
if (res != 0) {
fprintf(stderr, "[M::%s] ERROR during mapping %s (check files exists and are amino acid fastas)\n", __func__, argv[i]);
return 1;
}
}
mp_idx_destroy(mi);
if (mp_verbose >= 3) {
fprintf(stderr, "[M::%s] Version: %s\n", __func__, MP_VERSION);
fprintf(stderr, "[M::%s] CMD:", __func__);
for (i = 0; i < argc; ++i)
fprintf(stderr, " %s", argv[i]);
fprintf(stderr, "\n[M::%s] Real time: %.3f sec; CPU: %.3f sec; Peak RSS: %.3f GB\n", __func__, mp_realtime(), mp_cputime(), mp_peakrss() / 1024.0 / 1024.0 / 1024.0);
}
return 0;
}