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Merge branch 'master' into utec

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This commit is contained in:
Heng Li
2021-07-16 13:32:47 -04:00
parent 28a37a017a 581f2d7123
commit b046052d82
39 changed files with 2143 additions and 531 deletions
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main.c
+33 -13
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@@ -7,7 +7,7 @@
#include "mmpriv.h"
#include "ketopt.h"
#define MM_VERSION "2.17-r987-qs-dirty"
#define MM_VERSION "2.21-r1071-qs-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -70,7 +70,9 @@ static ko_longopt_t long_options[] = {
{ "chain-gap-scale",ko_required_argument, 343 },
{ "alt", ko_required_argument, 344 },
{ "alt-drop", ko_required_argument, 345 },
{ "qstrand", ko_no_argument, 346 },
{ "mask-len", ko_required_argument, 346 },
{ "rmq", ko_optional_argument, 347 },
{ "qstrand", ko_no_argument, 348 },
{ "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' },
{ "version", ko_no_argument, 'V' },
@@ -82,17 +84,23 @@ static ko_longopt_t long_options[] = {
{ 0, 0, 0 }
};
static inline int64_t mm_parse_num(const char *str)
static inline int64_t mm_parse_num2(const char *str, char **q)
{
double x;
char *p;
x = strtod(str, &p);
if (*p == 'G' || *p == 'g') x *= 1e9;
else if (*p == 'M' || *p == 'm') x *= 1e6;
else if (*p == 'K' || *p == 'k') x *= 1e3;
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 mm_parse_num(const char *str)
{
return mm_parse_num2(str, 0);
}
static inline void yes_or_no(mm_mapopt_t *opt, int flag, int long_idx, const char *arg, int yes_to_set)
{
if (yes_to_set) {
@@ -108,7 +116,7 @@ static inline void yes_or_no(mm_mapopt_t *opt, int flag, int long_idx, const cha
int main(int argc, char *argv[])
{
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:yYPo:";
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:yYPo:e:U:";
ketopt_t o = KETOPT_INIT;
mm_mapopt_t opt;
mm_idxopt_t ipt;
@@ -144,7 +152,6 @@ int main(int argc, char *argv[])
else if (c == 'k') ipt.k = atoi(o.arg);
else if (c == 'H') ipt.flag |= MM_I_HPC;
else if (c == 'd') fnw = o.arg; // the above are indexing related options, except -I
else if (c == 'r') opt.bw = (int)mm_parse_num(o.arg);
else if (c == 't') n_threads = atoi(o.arg);
else if (c == 'v') mm_verbose = atoi(o.arg);
else if (c == 'g') opt.max_gap = (int)mm_parse_num(o.arg);
@@ -171,6 +178,7 @@ int main(int argc, char *argv[])
else if (c == 'C') opt.noncan = atoi(o.arg);
else if (c == 'I') ipt.batch_size = mm_parse_num(o.arg);
else if (c == 'K') opt.mini_batch_size = mm_parse_num(o.arg);
else if (c == 'e') opt.occ_dist = mm_parse_num(o.arg);
else if (c == 'R') rg = o.arg;
else if (c == 'h') fp_help = stdout;
else if (c == '2') opt.flag |= MM_F_2_IO_THREADS;
@@ -203,7 +211,6 @@ int main(int argc, char *argv[])
else if (c == 327) opt.max_clip_ratio = atof(o.arg); // --max-clip-ratio
else if (c == 328) opt.min_mid_occ = atoi(o.arg); // --min-occ-floor
else if (c == 329) opt.flag |= MM_F_OUT_MD; // --MD
else if (c == 330) opt.min_join_flank_ratio = atof(o.arg); // --lj-min-ratio
else if (c == 331) opt.sc_ambi = atoi(o.arg); // --score-N
else if (c == 332) opt.flag |= MM_F_EQX; // --eqx
else if (c == 333) opt.flag |= MM_F_PAF_NO_HIT; // --paf-no-hit
@@ -218,8 +225,11 @@ int main(int argc, char *argv[])
else if (c == 343) opt.chain_gap_scale = atof(o.arg); // --chain-gap-scale
else if (c == 344) alt_list = o.arg; // --alt
else if (c == 345) opt.alt_drop = atof(o.arg); // --alt-drop
else if (c == 346) opt.flag |= MM_F_QSTRAND | MM_F_NO_INV; // --qstrand
else if (c == 314) { // --frag
else if (c == 346) opt.mask_len = mm_parse_num(o.arg); // --mask-len
else if (c == 348) opt.flag |= MM_F_QSTRAND | MM_F_NO_INV; // --qstrand
else if (c == 330) {
fprintf(stderr, "[WARNING] \033[1;31m --lj-min-ratio has been deprecated.\033[0m\n");
} else if (c == 314) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
} else if (c == 315) { // --secondary
yes_or_no(&opt, MM_F_NO_PRINT_2ND, o.longidx, o.arg, 0);
@@ -240,6 +250,8 @@ int main(int argc, char *argv[])
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 == 347) { // --rmq
yes_or_no(&opt, MM_F_RMQ, o.longidx, o.arg, 1);
} else if (c == 'S') {
opt.flag |= MM_F_OUT_CS | MM_F_CIGAR | MM_F_OUT_CS_LONG;
if (mm_verbose >= 2)
@@ -247,6 +259,12 @@ int main(int argc, char *argv[])
} else if (c == 'V') {
puts(MM_VERSION);
return 0;
} else if (c == 'r') {
opt.bw = (int)mm_parse_num2(o.arg, &s);
if (*s == ',') opt.bw_long = (int)mm_parse_num2(s + 1, &s);
} else if (c == 'U') {
opt.min_mid_occ = strtol(o.arg, &s, 10);
if (*s == ',') opt.max_mid_occ = strtol(s + 1, &s, 10);
} else if (c == 'f') {
double x;
char *p;
@@ -301,7 +319,7 @@ int main(int argc, char *argv[])
fprintf(fp_help, " -g NUM stop chain enlongation if there are no minimizers in INT-bp [%d]\n", opt.max_gap);
fprintf(fp_help, " -G NUM max intron length (effective with -xsplice; changing -r) [200k]\n");
fprintf(fp_help, " -F NUM max fragment length (effective with -xsr or in the fragment mode) [800]\n");
fprintf(fp_help, " -r NUM bandwidth used in chaining and DP-based alignment [%d]\n", opt.bw);
fprintf(fp_help, " -r NUM[,NUM] chaining/alignment bandwidth and long-join bandwidth [%d,%d]\n", opt.bw, opt.bw_long);
fprintf(fp_help, " -n INT minimal number of minimizers on a chain [%d]\n", opt.min_cnt);
fprintf(fp_help, " -m INT minimal chaining score (matching bases minus log gap penalty) [%d]\n", opt.min_chain_score);
// fprintf(fp_help, " -T INT SDUST threshold; 0 to disable SDUST [%d]\n", opt.sdust_thres); // TODO: this option is never used; might be buggy
@@ -332,7 +350,8 @@ int main(int argc, char *argv[])
fprintf(fp_help, " --version show version number\n");
fprintf(fp_help, " Preset:\n");
fprintf(fp_help, " -x STR preset (always applied before other options; see minimap2.1 for details) []\n");
fprintf(fp_help, " - map-pb/map-ont - PacBio/Nanopore vs reference mapping\n");
fprintf(fp_help, " - map-pb/map-ont - PacBio CLR/Nanopore vs reference mapping\n");
fprintf(fp_help, " - map-hifi - PacBio HiFi reads vs reference mapping\n");
fprintf(fp_help, " - ava-pb/ava-ont - PacBio/Nanopore read overlap\n");
fprintf(fp_help, " - asm5/asm10/asm20 - asm-to-ref mapping, for ~0.1/1/5%% sequence divergence\n");
fprintf(fp_help, " - splice/splice:hq - long-read/Pacbio-CCS spliced alignment\n");
@@ -389,6 +408,7 @@ int main(int argc, char *argv[])
if (mm_verbose >= 3) mm_idx_stat(mi);
if (junc_bed) mm_idx_bed_read(mi, junc_bed, 1);
if (alt_list) mm_idx_alt_read(mi, alt_list);
if (argc - (o.ind + 1) == 0) continue; // no query files
ret = 0;
if (!(opt.flag & MM_F_FRAG_MODE)) {
for (i = o.ind + 1; i < argc; ++i) {