mirror of
https://github.com/lh3/minimap2.git
synced 2026-10-08 16:58:12 +08:00
r829: replaced musl's getopt with ketopt
This commit is contained in:
Heng Li
@@ -4,13 +4,9 @@
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#include "bseq.h"
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#include "minimap.h"
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#include "mmpriv.h"
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#ifdef HAVE_GETOPT
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#include <getopt.h>
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#else
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#include "getopt.h"
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#endif
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#include "ketopt.h"
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#define MM_VERSION "2.12-r828-dirty"
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#define MM_VERSION "2.12-r829-dirty"
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#ifdef __linux__
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#include <sys/resource.h>
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@@ -26,52 +22,52 @@ void liftrlimit()
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void liftrlimit() {}
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#endif
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static struct option long_options[] = {
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{ "bucket-bits", required_argument, 0, 0 },
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{ "mb-size", required_argument, 0, 'K' },
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{ "seed", required_argument, 0, 0 },
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{ "no-kalloc", no_argument, 0, 0 },
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{ "print-qname", no_argument, 0, 0 },
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{ "no-self", no_argument, 0, 'D' },
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{ "print-seeds", no_argument, 0, 0 },
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{ "max-chain-skip", required_argument, 0, 0 },
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{ "min-dp-len", required_argument, 0, 0 },
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{ "print-aln-seq", no_argument, 0, 0 },
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{ "splice", no_argument, 0, 0 },
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{ "cost-non-gt-ag", required_argument, 0, 'C' },
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{ "no-long-join", no_argument, 0, 0 },
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{ "sr", no_argument, 0, 0 },
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{ "frag", required_argument, 0, 0 },
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{ "secondary", required_argument, 0, 0 },
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{ "cs", optional_argument, 0, 0 },
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{ "end-bonus", required_argument, 0, 0 },
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{ "no-pairing", no_argument, 0, 0 },
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{ "splice-flank", required_argument, 0, 0 },
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{ "idx-no-seq", no_argument, 0, 0 },
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{ "end-seed-pen", required_argument, 0, 0 }, // 21
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{ "for-only", no_argument, 0, 0 }, // 22
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{ "rev-only", no_argument, 0, 0 }, // 23
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{ "heap-sort", required_argument, 0, 0 }, // 24
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{ "all-chain", no_argument, 0, 'P' },
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{ "dual", required_argument, 0, 0 }, // 26
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{ "max-clip-ratio", required_argument, 0, 0 }, // 27
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{ "min-occ-floor", required_argument, 0, 0 }, // 28
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{ "MD", no_argument, 0, 0 }, // 29
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{ "lj-min-ratio", required_argument, 0, 0 }, // 30
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{ "score-N", required_argument, 0, 0 }, // 31
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{ "eqx", no_argument, 0, 0 }, // 32
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{ "paf-no-hit", no_argument, 0, 0 }, // 33
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{ "split-prefix", required_argument, 0, 0 }, // 34
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{ "no-end-flt", no_argument, 0, 0 }, // 35
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{ "help", no_argument, 0, 'h' },
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{ "max-intron-len", required_argument, 0, 'G' },
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{ "version", no_argument, 0, 'V' },
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{ "min-count", required_argument, 0, 'n' },
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{ "min-chain-score",required_argument, 0, 'm' },
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{ "mask-level", required_argument, 0, 'M' },
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{ "min-dp-score", required_argument, 0, 's' },
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{ "sam", no_argument, 0, 'a' },
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{ 0, 0, 0, 0}
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static ko_longopt_t long_options[] = {
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{ "bucket-bits", ko_required_argument, 300 },
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{ "mb-size", ko_required_argument, 'K' },
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{ "seed", ko_required_argument, 302 },
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{ "no-kalloc", ko_no_argument, 303 },
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{ "print-qname", ko_no_argument, 304 },
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{ "no-self", ko_no_argument, 'D' },
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{ "print-seeds", ko_no_argument, 306 },
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{ "max-chain-skip", ko_required_argument, 307 },
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{ "min-dp-len", ko_required_argument, 308 },
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{ "print-aln-seq", ko_no_argument, 309 },
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{ "splice", ko_no_argument, 310 },
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{ "cost-non-gt-ag", ko_required_argument, 'C' },
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{ "no-long-join", ko_no_argument, 312 },
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{ "sr", ko_no_argument, 313 },
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{ "frag", ko_required_argument, 314 },
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{ "secondary", ko_required_argument, 315 },
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{ "cs", ko_optional_argument, 316 },
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{ "end-bonus", ko_required_argument, 317 },
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{ "no-pairing", ko_no_argument, 318 },
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{ "splice-flank", ko_required_argument, 319 },
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{ "idx-no-seq", ko_no_argument, 320 },
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{ "end-seed-pen", ko_required_argument, 321 },
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{ "for-only", ko_no_argument, 322 },
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{ "rev-only", ko_no_argument, 323 },
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{ "heap-sort", ko_required_argument, 324 },
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{ "all-chain", ko_no_argument, 'P' },
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{ "dual", ko_required_argument, 326 },
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{ "max-clip-ratio", ko_required_argument, 327 },
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{ "min-occ-floor", ko_required_argument, 328 },
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{ "MD", ko_no_argument, 329 },
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{ "lj-min-ratio", ko_required_argument, 330 },
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{ "score-N", ko_required_argument, 331 },
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{ "eqx", ko_no_argument, 332 },
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{ "paf-no-hit", ko_no_argument, 333 },
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{ "split-prefix", ko_required_argument, 334 },
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{ "no-end-flt", ko_no_argument, 335 },
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{ "help", ko_no_argument, 'h' },
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{ "max-intron-len", ko_required_argument, 'G' },
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{ "version", ko_no_argument, 'V' },
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{ "min-count", ko_required_argument, 'n' },
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{ "min-chain-score",ko_required_argument, 'm' },
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{ "mask-level", ko_required_argument, 'M' },
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{ "min-dp-score", ko_required_argument, 's' },
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{ "sam", ko_no_argument, 'a' },
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{ 0, 0, 0 }
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};
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static inline int64_t mm_parse_num(const char *str)
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@@ -101,9 +97,10 @@ static inline void yes_or_no(mm_mapopt_t *opt, int flag, int long_idx, const cha
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int main(int argc, char *argv[])
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{
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const char *opt_str = "2aSDw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:LC:yY";
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ketopt_t o = KETOPT_INIT;
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mm_mapopt_t opt;
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mm_idxopt_t ipt;
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int i, c, n_threads = 3, n_parts, long_idx;
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int i, c, n_threads = 3, n_parts;
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char *fnw = 0, *rg = 0, *s;
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FILE *fp_help = stderr;
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mm_idx_reader_t *idx_rdr;
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@@ -114,30 +111,36 @@ int main(int argc, char *argv[])
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mm_realtime0 = realtime();
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mm_set_opt(0, &ipt, &opt);
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while ((c = getopt_long(argc, argv, opt_str, long_options, &long_idx)) >= 0) // apply option -x/preset first
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while ((c = ketopt(&o, argc, argv, 1, opt_str, long_options)) >= 0) { // test command line options and apply option -x/preset first
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if (c == 'x') {
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if (mm_set_opt(optarg, &ipt, &opt) < 0) {
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fprintf(stderr, "[ERROR] unknown preset '%s'\n", optarg);
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if (mm_set_opt(o.arg, &ipt, &opt) < 0) {
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fprintf(stderr, "[ERROR] unknown preset '%s'\n", o.arg);
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return 1;
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}
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break;
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} else if (c == ':') {
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fprintf(stderr, "[ERROR] missing option argument\n");
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return 1;
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} else if (c == '?') {
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fprintf(stderr, "[ERROR] unknown option in \"%s\"\n", argv[o.i]);
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return 1;
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}
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optind = 0; // for musl getopt, optind=0 has the same effect as optreset=1; older libc doesn't have optreset
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}
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o = KETOPT_INIT;
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while ((c = getopt_long(argc, argv, opt_str, long_options, &long_idx)) >= 0) {
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if (c == 'w') ipt.w = atoi(optarg);
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else if (c == 'k') ipt.k = atoi(optarg);
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while ((c = ketopt(&o, argc, argv, 1, opt_str, long_options)) >= 0) {
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if (c == 'w') ipt.w = atoi(o.arg);
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else if (c == 'k') ipt.k = atoi(o.arg);
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else if (c == 'H') ipt.flag |= MM_I_HPC;
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else if (c == 'd') fnw = optarg; // the above are indexing related options, except -I
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else if (c == 'r') opt.bw = (int)mm_parse_num(optarg);
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else if (c == 't') n_threads = atoi(optarg);
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else if (c == 'v') mm_verbose = atoi(optarg);
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else if (c == 'g') opt.max_gap = (int)mm_parse_num(optarg);
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else if (c == 'G') mm_mapopt_max_intron_len(&opt, (int)mm_parse_num(optarg));
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else if (c == 'F') opt.max_frag_len = (int)mm_parse_num(optarg);
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else if (c == 'N') opt.best_n = atoi(optarg);
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else if (c == 'p') opt.pri_ratio = atof(optarg);
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else if (c == 'M') opt.mask_level = atof(optarg);
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else if (c == 'd') fnw = o.arg; // the above are indexing related options, except -I
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else if (c == 'r') opt.bw = (int)mm_parse_num(o.arg);
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else if (c == 't') n_threads = atoi(o.arg);
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else if (c == 'v') mm_verbose = atoi(o.arg);
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else if (c == 'g') opt.max_gap = (int)mm_parse_num(o.arg);
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else if (c == 'G') mm_mapopt_max_intron_len(&opt, (int)mm_parse_num(o.arg));
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else if (c == 'F') opt.max_frag_len = (int)mm_parse_num(o.arg);
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else if (c == 'N') opt.best_n = atoi(o.arg);
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else if (c == 'p') opt.pri_ratio = atof(o.arg);
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else if (c == 'M') opt.mask_level = atof(o.arg);
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else if (c == 'c') opt.flag |= MM_F_OUT_CG | MM_F_CIGAR;
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else if (c == 'D') opt.flag |= MM_F_NO_DIAG;
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else if (c == 'P') opt.flag |= MM_F_ALL_CHAINS;
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@@ -147,65 +150,65 @@ int main(int argc, char *argv[])
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else if (c == 'Y') opt.flag |= MM_F_SOFTCLIP;
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else if (c == 'L') opt.flag |= MM_F_LONG_CIGAR;
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else if (c == 'y') opt.flag |= MM_F_COPY_COMMENT;
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else if (c == 'T') opt.sdust_thres = atoi(optarg);
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else if (c == 'n') opt.min_cnt = atoi(optarg);
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else if (c == 'm') opt.min_chain_score = atoi(optarg);
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else if (c == 'A') opt.a = atoi(optarg);
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else if (c == 'B') opt.b = atoi(optarg);
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else if (c == 's') opt.min_dp_max = atoi(optarg);
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else if (c == 'C') opt.noncan = atoi(optarg);
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else if (c == 'I') ipt.batch_size = mm_parse_num(optarg);
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else if (c == 'K') opt.mini_batch_size = (int)mm_parse_num(optarg);
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else if (c == 'R') rg = optarg;
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else if (c == 'T') opt.sdust_thres = atoi(o.arg);
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else if (c == 'n') opt.min_cnt = atoi(o.arg);
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else if (c == 'm') opt.min_chain_score = atoi(o.arg);
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else if (c == 'A') opt.a = atoi(o.arg);
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else if (c == 'B') opt.b = atoi(o.arg);
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else if (c == 's') opt.min_dp_max = atoi(o.arg);
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else if (c == 'C') opt.noncan = atoi(o.arg);
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else if (c == 'I') ipt.batch_size = mm_parse_num(o.arg);
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else if (c == 'K') opt.mini_batch_size = (int)mm_parse_num(o.arg);
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else if (c == 'R') rg = o.arg;
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else if (c == 'h') fp_help = stdout;
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else if (c == '2') opt.flag |= MM_F_2_IO_THREADS;
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else if (c == 0 && long_idx == 0) ipt.bucket_bits = atoi(optarg); // --bucket-bits
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else if (c == 0 && long_idx == 2) opt.seed = atoi(optarg); // --seed
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else if (c == 0 && long_idx == 3) mm_dbg_flag |= MM_DBG_NO_KALLOC; // --no-kalloc
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else if (c == 0 && long_idx == 4) mm_dbg_flag |= MM_DBG_PRINT_QNAME; // --print-qname
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else if (c == 0 && long_idx == 6) mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_SEED, n_threads = 1; // --print-seed
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else if (c == 0 && long_idx == 7) opt.max_chain_skip = atoi(optarg); // --max-chain-skip
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else if (c == 0 && long_idx == 8) opt.min_ksw_len = atoi(optarg); // --min-dp-len
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else if (c == 0 && long_idx == 9) mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_ALN_SEQ, n_threads = 1; // --print-aln-seq
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else if (c == 0 && long_idx ==10) opt.flag |= MM_F_SPLICE; // --splice
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else if (c == 0 && long_idx ==12) opt.flag |= MM_F_NO_LJOIN; // --no-long-join
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else if (c == 0 && long_idx ==13) opt.flag |= MM_F_SR; // --sr
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else if (c == 0 && long_idx ==17) opt.end_bonus = atoi(optarg); // --end-bonus
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else if (c == 0 && long_idx ==18) opt.flag |= MM_F_INDEPEND_SEG; // --no-pairing
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else if (c == 0 && long_idx ==20) ipt.flag |= MM_I_NO_SEQ; // --idx-no-seq
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else if (c == 0 && long_idx ==21) opt.anchor_ext_shift = atoi(optarg); // --end-seed-pen
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else if (c == 0 && long_idx ==22) opt.flag |= MM_F_FOR_ONLY; // --for-only
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else if (c == 0 && long_idx ==23) opt.flag |= MM_F_REV_ONLY; // --rev-only
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else if (c == 0 && long_idx ==27) opt.max_clip_ratio = atof(optarg); // --max-clip-ratio
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else if (c == 0 && long_idx ==28) opt.min_mid_occ = atoi(optarg); // --min-occ-floor
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else if (c == 0 && long_idx ==29) opt.flag |= MM_F_OUT_MD; // --MD
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else if (c == 0 && long_idx ==30) opt.min_join_flank_ratio = atof(optarg); // --lj-min-ratio
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else if (c == 0 && long_idx ==31) opt.sc_ambi = atoi(optarg); // --score-N
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else if (c == 0 && long_idx ==32) opt.flag |= MM_F_EQX; // --eqx
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else if (c == 0 && long_idx ==33) opt.flag |= MM_F_PAF_NO_HIT; // --paf-no-hit
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else if (c == 0 && long_idx ==34) opt.split_prefix = optarg; // --split-prefix
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else if (c == 0 && long_idx ==35) opt.flag |= MM_F_NO_END_FLT; // --no-end-flt
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else if (c == 0 && long_idx == 14) { // --frag
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yes_or_no(&opt, MM_F_FRAG_MODE, long_idx, optarg, 1);
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} else if (c == 0 && long_idx == 15) { // --secondary
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yes_or_no(&opt, MM_F_NO_PRINT_2ND, long_idx, optarg, 0);
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} else if (c == 0 && long_idx == 16) { // --cs
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else if (c == 300) ipt.bucket_bits = atoi(o.arg); // --bucket-bits
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else if (c == 302) opt.seed = atoi(o.arg); // --seed
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else if (c == 303) mm_dbg_flag |= MM_DBG_NO_KALLOC; // --no-kalloc
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else if (c == 304) mm_dbg_flag |= MM_DBG_PRINT_QNAME; // --print-qname
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else if (c == 306) mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_SEED, n_threads = 1; // --print-seed
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else if (c == 307) opt.max_chain_skip = atoi(o.arg); // --max-chain-skip
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else if (c == 308) opt.min_ksw_len = atoi(o.arg); // --min-dp-len
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else if (c == 309) mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_ALN_SEQ, n_threads = 1; // --print-aln-seq
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else if (c == 310) opt.flag |= MM_F_SPLICE; // --splice
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else if (c == 312) opt.flag |= MM_F_NO_LJOIN; // --no-long-join
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else if (c == 313) opt.flag |= MM_F_SR; // --sr
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else if (c == 317) opt.end_bonus = atoi(o.arg); // --end-bonus
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else if (c == 318) opt.flag |= MM_F_INDEPEND_SEG; // --no-pairing
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else if (c == 320) ipt.flag |= MM_I_NO_SEQ; // --idx-no-seq
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else if (c == 321) opt.anchor_ext_shift = atoi(o.arg); // --end-seed-pen
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else if (c == 322) opt.flag |= MM_F_FOR_ONLY; // --for-only
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else if (c == 323) opt.flag |= MM_F_REV_ONLY; // --rev-only
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else if (c == 327) opt.max_clip_ratio = atof(o.arg); // --max-clip-ratio
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else if (c == 328) opt.min_mid_occ = atoi(o.arg); // --min-occ-floor
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else if (c == 329) opt.flag |= MM_F_OUT_MD; // --MD
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else if (c == 330) opt.min_join_flank_ratio = atof(o.arg); // --lj-min-ratio
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else if (c == 331) opt.sc_ambi = atoi(o.arg); // --score-N
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else if (c == 332) opt.flag |= MM_F_EQX; // --eqx
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else if (c == 333) opt.flag |= MM_F_PAF_NO_HIT; // --paf-no-hit
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else if (c == 334) opt.split_prefix = o.arg; // --split-prefix
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else if (c == 335) opt.flag |= MM_F_NO_END_FLT; // --no-end-flt
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else if (c == 314) { // --frag
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yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
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} else if (c == 315) { // --secondary
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yes_or_no(&opt, MM_F_NO_PRINT_2ND, o.longidx, o.arg, 0);
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} else if (c == 316) { // --cs
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opt.flag |= MM_F_OUT_CS | MM_F_CIGAR;
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if (optarg == 0 || strcmp(optarg, "short") == 0) {
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if (o.arg == 0 || strcmp(o.arg, "short") == 0) {
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opt.flag &= ~MM_F_OUT_CS_LONG;
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} else if (strcmp(optarg, "long") == 0) {
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} else if (strcmp(o.arg, "long") == 0) {
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opt.flag |= MM_F_OUT_CS_LONG;
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} else if (strcmp(optarg, "none") == 0) {
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} else if (strcmp(o.arg, "none") == 0) {
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opt.flag &= ~MM_F_OUT_CS;
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} else if (mm_verbose >= 2) {
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fprintf(stderr, "[WARNING]\033[1;31m --cs only takes 'short' or 'long'. Invalid values are assumed to be 'short'.\033[0m\n");
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}
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} else if (c == 0 && long_idx == 19) { // --splice-flank
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yes_or_no(&opt, MM_F_SPLICE_FLANK, long_idx, optarg, 1);
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} else if (c == 0 && long_idx == 24) { // --heap-sort
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yes_or_no(&opt, MM_F_HEAP_SORT, long_idx, optarg, 1);
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} else if (c == 0 && long_idx == 26) { // --dual
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yes_or_no(&opt, MM_F_NO_DUAL, long_idx, optarg, 0);
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} else if (c == 319) { // --splice-flank
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yes_or_no(&opt, MM_F_SPLICE_FLANK, o.longidx, o.arg, 1);
|
||||
} else if (c == 324) { // --heap-sort
|
||||
yes_or_no(&opt, MM_F_HEAP_SORT, o.longidx, o.arg, 1);
|
||||
} else if (c == 326) { // --dual
|
||||
yes_or_no(&opt, MM_F_NO_DUAL, o.longidx, o.arg, 0);
|
||||
} else if (c == 'S') {
|
||||
opt.flag |= MM_F_OUT_CS | MM_F_CIGAR | MM_F_OUT_CS_LONG;
|
||||
if (mm_verbose >= 2)
|
||||
@@ -216,27 +219,27 @@ int main(int argc, char *argv[])
|
||||
} else if (c == 'f') {
|
||||
double x;
|
||||
char *p;
|
||||
x = strtod(optarg, &p);
|
||||
x = strtod(o.arg, &p);
|
||||
if (x < 1.0) opt.mid_occ_frac = x, opt.mid_occ = 0;
|
||||
else opt.mid_occ = (int)(x + .499);
|
||||
if (*p == ',') opt.max_occ = (int)(strtod(p+1, &p) + .499);
|
||||
} else if (c == 'u') {
|
||||
if (*optarg == 'b') opt.flag |= MM_F_SPLICE_FOR|MM_F_SPLICE_REV; // both strands
|
||||
else if (*optarg == 'f') opt.flag |= MM_F_SPLICE_FOR, opt.flag &= ~MM_F_SPLICE_REV; // match GT-AG
|
||||
else if (*optarg == 'r') opt.flag |= MM_F_SPLICE_REV, opt.flag &= ~MM_F_SPLICE_FOR; // match CT-AC (reverse complement of GT-AG)
|
||||
else if (*optarg == 'n') opt.flag &= ~(MM_F_SPLICE_FOR|MM_F_SPLICE_REV); // don't try to match the GT-AG signal
|
||||
if (*o.arg == 'b') opt.flag |= MM_F_SPLICE_FOR|MM_F_SPLICE_REV; // both strands
|
||||
else if (*o.arg == 'f') opt.flag |= MM_F_SPLICE_FOR, opt.flag &= ~MM_F_SPLICE_REV; // match GT-AG
|
||||
else if (*o.arg == 'r') opt.flag |= MM_F_SPLICE_REV, opt.flag &= ~MM_F_SPLICE_FOR; // match CT-AC (reverse complement of GT-AG)
|
||||
else if (*o.arg == 'n') opt.flag &= ~(MM_F_SPLICE_FOR|MM_F_SPLICE_REV); // don't try to match the GT-AG signal
|
||||
else {
|
||||
fprintf(stderr, "[ERROR]\033[1;31m unrecognized cDNA direction\033[0m\n");
|
||||
return 1;
|
||||
}
|
||||
} else if (c == 'z') {
|
||||
opt.zdrop = opt.zdrop_inv = strtol(optarg, &s, 10);
|
||||
opt.zdrop = opt.zdrop_inv = strtol(o.arg, &s, 10);
|
||||
if (*s == ',') opt.zdrop_inv = strtol(s + 1, &s, 10);
|
||||
} else if (c == 'O') {
|
||||
opt.q = opt.q2 = strtol(optarg, &s, 10);
|
||||
opt.q = opt.q2 = strtol(o.arg, &s, 10);
|
||||
if (*s == ',') opt.q2 = strtol(s + 1, &s, 10);
|
||||
} else if (c == 'E') {
|
||||
opt.e = opt.e2 = strtol(optarg, &s, 10);
|
||||
opt.e = opt.e2 = strtol(o.arg, &s, 10);
|
||||
if (*s == ',') opt.e2 = strtol(s + 1, &s, 10);
|
||||
}
|
||||
}
|
||||
@@ -249,7 +252,7 @@ int main(int argc, char *argv[])
|
||||
if (mm_check_opt(&ipt, &opt) < 0)
|
||||
return 1;
|
||||
|
||||
if (argc == optind || fp_help == stdout) {
|
||||
if (argc == o.ind || fp_help == stdout) {
|
||||
fprintf(fp_help, "Usage: minimap2 [options] <target.fa>|<target.idx> [query.fa] [...]\n");
|
||||
fprintf(fp_help, "Options:\n");
|
||||
fprintf(fp_help, " Indexing:\n");
|
||||
@@ -303,16 +306,16 @@ int main(int argc, char *argv[])
|
||||
return fp_help == stdout? 0 : 1;
|
||||
}
|
||||
|
||||
if ((opt.flag & MM_F_SR) && argc - optind > 3) {
|
||||
if ((opt.flag & MM_F_SR) && argc - o.ind > 3) {
|
||||
fprintf(stderr, "[ERROR] incorrect input: in the sr mode, please specify no more than two query files.\n");
|
||||
return 1;
|
||||
}
|
||||
idx_rdr = mm_idx_reader_open(argv[optind], &ipt, fnw);
|
||||
idx_rdr = mm_idx_reader_open(argv[o.ind], &ipt, fnw);
|
||||
if (idx_rdr == 0) {
|
||||
fprintf(stderr, "[ERROR] failed to open file '%s'\n", argv[optind]);
|
||||
fprintf(stderr, "[ERROR] failed to open file '%s'\n", argv[o.ind]);
|
||||
return 1;
|
||||
}
|
||||
if (!idx_rdr->is_idx && fnw == 0 && argc - optind < 2) {
|
||||
if (!idx_rdr->is_idx && fnw == 0 && argc - o.ind < 2) {
|
||||
fprintf(stderr, "[ERROR] missing input: please specify a query file to map or option -d to keep the index\n");
|
||||
mm_idx_reader_close(idx_rdr);
|
||||
return 1;
|
||||
@@ -338,13 +341,13 @@ int main(int argc, char *argv[])
|
||||
if (mm_verbose >= 3)
|
||||
fprintf(stderr, "[M::%s::%.3f*%.2f] loaded/built the index for %d target sequence(s)\n",
|
||||
__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), mi->n_seq);
|
||||
if (argc != optind + 1) mm_mapopt_update(&opt, mi);
|
||||
if (argc != o.ind + 1) mm_mapopt_update(&opt, mi);
|
||||
if (mm_verbose >= 3) mm_idx_stat(mi);
|
||||
if (!(opt.flag & MM_F_FRAG_MODE)) {
|
||||
for (i = optind + 1; i < argc; ++i)
|
||||
for (i = o.ind + 1; i < argc; ++i)
|
||||
mm_map_file(mi, argv[i], &opt, n_threads);
|
||||
} else {
|
||||
mm_map_file_frag(mi, argc - (optind + 1), (const char**)&argv[optind + 1], &opt, n_threads);
|
||||
mm_map_file_frag(mi, argc - (o.ind + 1), (const char**)&argv[o.ind + 1], &opt, n_threads);
|
||||
}
|
||||
mm_idx_destroy(mi);
|
||||
}
|
||||
@@ -352,7 +355,7 @@ int main(int argc, char *argv[])
|
||||
mm_idx_reader_close(idx_rdr);
|
||||
|
||||
if (opt.split_prefix)
|
||||
mm_split_merge(argc - (optind + 1), (const char**)&argv[optind + 1], &opt, n_parts);
|
||||
mm_split_merge(argc - (o.ind + 1), (const char**)&argv[o.ind + 1], &opt, n_parts);
|
||||
|
||||
if (fflush(stdout) == EOF) {
|
||||
fprintf(stderr, "[ERROR] failed to write the results\n");
|
||||
|
||||
Reference in New Issue
Block a user