添加了一些统计运行时间的变量，测试性能
This commit is contained in:
zzh
parent
1641a66d15
commit
023c18ba32
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@ -0,0 +1,5 @@
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{
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"recommendations": [
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"mhutchie.git-graph"
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]
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}
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@ -10,12 +10,16 @@
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"type": "cppdbg",
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"request": "launch",
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"program": "${workspaceRoot}/minimap2",
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"args": ["-x",
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"ava-ont",
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"-t",
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"1",
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"/public/home/zzh/work/3gseq/TGM-2021YFF/Acinetobacter_pittii.fastq",
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"/public/home/zzh/work/3gseq/TGM-2021YFF/Acinetobacter_pittii.fastq"],
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"args": [
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"-x",
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"ava-ont",
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"-t",
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"1",
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"/public/home/zzh/work/3gseq/TGM-2021YFF/Acinetobacter_pittii.fastq",
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"/public/home/zzh/work/3gseq/TGM-2021YFF/Acinetobacter_pittii.fastq",
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"-o",
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"reads.paf"
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],
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"cwd": "${workspaceFolder}", // 当前工作路径：当前文件所在的工作空间
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}
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]
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@ -0,0 +1,6 @@
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{
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"files.associations": {
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"minimap.h": "c",
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"time.h": "c"
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}
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}
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3
Makefile
3
Makefile
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@ -1,4 +1,5 @@
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CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra
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CFLAGS= -g -Wall -Wc++-compat #-Wextra
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#CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra
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CPPFLAGS= -DHAVE_KALLOC
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INCLUDES=
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OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o \
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11
index.c
11
index.c
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@ -15,6 +15,11 @@
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#include "kvec.h"
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#include "khash.h"
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#ifdef ANALYSIS_PERF
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extern int64_t get_mseconds();
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extern int64_t time_mm_idx_reader_read;
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#endif
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#define idx_hash(a) ((a)>>1)
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#define idx_eq(a, b) ((a)>>1 == (b)>>1)
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KHASH_INIT(idx, uint64_t, uint64_t, 1, idx_hash, idx_eq)
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@ -608,6 +613,9 @@ void mm_idx_reader_close(mm_idx_reader_t *r)
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mm_idx_t *mm_idx_reader_read(mm_idx_reader_t *r, int n_threads)
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{
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mm_idx_t *mi;
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#ifdef ANALYSIS_PERF
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int64_t tmp_cur_time = get_mseconds();
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#endif
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if (r->is_idx) {
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mi = mm_idx_load(r->fp.idx);
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if (mi && mm_verbose >= 2 && (mi->k != r->opt.k || mi->w != r->opt.w || (mi->flag&MM_I_HPC) != (r->opt.flag&MM_I_HPC)))
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@ -618,6 +626,9 @@ mm_idx_t *mm_idx_reader_read(mm_idx_reader_t *r, int n_threads)
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if (r->fp_out) mm_idx_dump(r->fp_out, mi);
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mi->index = r->n_parts++;
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}
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#ifdef ANALYSIS_PERF
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time_mm_idx_reader_read += get_mseconds() - tmp_cur_time;
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#endif
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return mi;
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}
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22
lchain.c
22
lchain.c
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@ -5,7 +5,11 @@
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#include "mmpriv.h"
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#include "kalloc.h"
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#include "krmq.h"
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#ifdef ANALYSIS_PERF
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extern int64_t get_mseconds();
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extern int64_t time_mg_lchain_dp,
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time_mg_chain_backtrack;
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#endif
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static int64_t mg_chain_bk_end(int32_t max_drop, const mm128_t *z, const int32_t *f, const int64_t *p, int32_t *t, int64_t k)
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{
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int64_t i = z[k].y, end_i = -1, max_i = i;
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@ -151,7 +155,9 @@ mm128_t *mg_lchain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int
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int32_t *f, *t, *v, n_u, n_v, mmax_f = 0, max_drop = bw;
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int64_t *p, i, j, max_ii, st = 0, n_iter = 0;
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uint64_t *u;
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#ifdef ANALYSIS_PERF
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int64_t tmp_cur_time = get_mseconds(), tmp_diff = 0;
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#endif
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if (_u) *_u = 0, *n_u_ = 0;
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if (n == 0 || a == 0) {
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kfree(km, a);
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@ -205,10 +211,20 @@ mm128_t *mg_lchain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int
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max_ii = i;
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if (mmax_f < max_f) mmax_f = max_f;
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}
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#ifdef ANALYSIS_PERF
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int64_t tmp_inner_time = get_mseconds();
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#endif
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u = mg_chain_backtrack(km, n, f, p, v, t, min_cnt, min_sc, max_drop, &n_u, &n_v);
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#ifdef ANALYSIS_PERF
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tmp_diff = get_mseconds() - tmp_inner_time;
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__sync_fetch_and_add(&time_mg_chain_backtrack, tmp_diff);
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#endif
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*n_u_ = n_u, *_u = u; // NB: note that u[] may not be sorted by score here
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kfree(km, p); kfree(km, f); kfree(km, t);
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#ifdef ANALYSIS_PERF
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tmp_diff = get_mseconds() - tmp_cur_time;
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__sync_fetch_and_add(&time_mg_lchain_dp, tmp_diff);
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#endif
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if (n_u == 0) {
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kfree(km, a); kfree(km, v);
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return 0;
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727
main.c
727
main.c
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@ -7,6 +7,38 @@
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#include "mmpriv.h"
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#include "ketopt.h"
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// 用来调试，计算感兴趣部分的运行时间
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#include "sys/time.h"
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// 获取当前毫秒数
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int64_t get_mseconds()
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{
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struct timeval tv;
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gettimeofday(&tv, NULL);
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return (int64_t)1000 * (tv.tv_sec + ((1e-6) * tv.tv_usec));
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}
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// 记录运行时间的变量
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#ifdef ANALYSIS_PERF
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int64_t time_mm_idx_reader_read,
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time_mm_map_file_frag,
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time_map_work_for_block_1,
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time_map_work_for_block_2,
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time_map_work_for_block_3,
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time_mm_map_frag_b1,
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time_mm_map_frag_b2,
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time_mm_map_frag_b3,
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time_mm_map_frag_b4,
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time_mm_map_frag_b5,
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time_mm_map_frag_b6,
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time_mg_lchain_dp = 0,
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time_collect_seed_hits_heap = 0,
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time_collect_seed_hits = 0,
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time_mg_chain_backtrack = 0;
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#endif
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//////////////////////////////////
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#ifdef __linux__
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#include <sys/resource.h>
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#include <sys/time.h>
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@ -18,85 +50,90 @@ void liftrlimit()
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setrlimit(RLIMIT_AS, &r);
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}
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#else
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void liftrlimit() {}
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void liftrlimit()
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{
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}
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#endif
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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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{ "hard-mask-level",ko_no_argument, 336 },
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{ "cap-sw-mem", ko_required_argument, 337 },
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{ "max-qlen", ko_required_argument, 338 },
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{ "max-chain-iter", ko_required_argument, 339 },
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{ "junc-bed", ko_required_argument, 340 },
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{ "junc-bonus", ko_required_argument, 341 },
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{ "sam-hit-only", ko_no_argument, 342 },
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{ "chain-gap-scale",ko_required_argument, 343 },
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{ "alt", ko_required_argument, 344 },
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{ "alt-drop", ko_required_argument, 345 },
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{ "mask-len", ko_required_argument, 346 },
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{ "rmq", ko_optional_argument, 347 },
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{ "qstrand", ko_no_argument, 348 },
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{ "cap-kalloc", ko_required_argument, 349 },
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{ "q-occ-frac", ko_required_argument, 350 },
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{ "chain-skip-scale",ko_required_argument,351 },
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{ "print-chains", ko_no_argument, 352 },
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{ "no-hash-name", ko_no_argument, 353 },
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{ "secondary-seq", ko_no_argument, 354 },
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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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{"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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{"hard-mask-level", ko_no_argument, 336},
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{"cap-sw-mem", ko_required_argument, 337},
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{"max-qlen", ko_required_argument, 338},
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{"max-chain-iter", ko_required_argument, 339},
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{"junc-bed", ko_required_argument, 340},
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{"junc-bonus", ko_required_argument, 341},
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{"sam-hit-only", ko_no_argument, 342},
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{"chain-gap-scale", ko_required_argument, 343},
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{"alt", ko_required_argument, 344},
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{"alt-drop", ko_required_argument, 345},
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{"mask-len", ko_required_argument, 346},
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{"rmq", ko_optional_argument, 347},
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{"qstrand", ko_no_argument, 348},
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{"cap-kalloc", ko_required_argument, 349},
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{"q-occ-frac", ko_required_argument, 350},
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{"chain-skip-scale", ko_required_argument, 351},
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{"print-chains", ko_no_argument, 352},
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{"no-hash-name", ko_no_argument, 353},
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{"secondary-seq", ko_no_argument, 354},
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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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static inline int64_t mm_parse_num2(const char *str, char **q)
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{
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double x;
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char *p;
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x = strtod(str, &p);
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if (*p == 'G' || *p == 'g') x *= 1e9, ++p;
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else if (*p == 'M' || *p == 'm') x *= 1e6, ++p;
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else if (*p == 'K' || *p == 'k') x *= 1e3, ++p;
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if (q) *q = p;
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if (*p == 'G' || *p == 'g')
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x *= 1e9, ++p;
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else if (*p == 'M' || *p == 'm')
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x *= 1e6, ++p;
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else if (*p == 'K' || *p == 'k')
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x *= 1e3, ++p;
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if (q)
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*q = p;
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return (int64_t)(x + .499);
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}
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@ -107,14 +144,23 @@ static inline int64_t mm_parse_num(const char *str)
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static inline void yes_or_no(mm_mapopt_t *opt, int64_t flag, int long_idx, const char *arg, int yes_to_set)
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{
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if (yes_to_set) {
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if (strcmp(arg, "yes") == 0 || strcmp(arg, "y") == 0) opt->flag |= flag;
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else if (strcmp(arg, "no") == 0 || strcmp(arg, "n") == 0) opt->flag &= ~flag;
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else fprintf(stderr, "[WARNING]\033[1;31m option '--%s' only accepts 'yes' or 'no'.\033[0m\n", long_options[long_idx].name);
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} else {
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if (strcmp(arg, "yes") == 0 || strcmp(arg, "y") == 0) opt->flag &= ~flag;
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else if (strcmp(arg, "no") == 0 || strcmp(arg, "n") == 0) opt->flag |= flag;
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else fprintf(stderr, "[WARNING]\033[1;31m option '--%s' only accepts 'yes' or 'no'.\033[0m\n", long_options[long_idx].name);
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if (yes_to_set)
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{
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if (strcmp(arg, "yes") == 0 || strcmp(arg, "y") == 0)
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opt->flag |= flag;
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else if (strcmp(arg, "no") == 0 || strcmp(arg, "n") == 0)
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opt->flag &= ~flag;
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else
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fprintf(stderr, "[WARNING]\033[1;31m option '--%s' only accepts 'yes' or 'no'.\033[0m\n", long_options[long_idx].name);
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}
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else
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{
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if (strcmp(arg, "yes") == 0 || strcmp(arg, "y") == 0)
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opt->flag &= ~flag;
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else if (strcmp(arg, "no") == 0 || strcmp(arg, "n") == 0)
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opt->flag |= flag;
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else
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fprintf(stderr, "[WARNING]\033[1;31m option '--%s' only accepts 'yes' or 'no'.\033[0m\n", long_options[long_idx].name);
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}
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}
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@ -135,194 +181,360 @@ 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 = 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(o.arg, &ipt, &opt) < 0) {
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#ifdef ANALYSIS_PERF
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time_mm_idx_reader_read = 0;
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time_mm_map_file_frag = 0;
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time_map_work_for_block_1 = 0;
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time_map_work_for_block_2 = 0;
|
||||
time_map_work_for_block_3 = 0;
|
||||
time_mm_map_frag_b1 = 0;
|
||||
time_mm_map_frag_b2 = 0;
|
||||
time_mm_map_frag_b3 = 0;
|
||||
time_mm_map_frag_b4 = 0;
|
||||
time_mm_map_frag_b5 = 0;
|
||||
time_mm_map_frag_b6 = 0;
|
||||
|
||||
#endif
|
||||
while ((c = ketopt(&o, argc, argv, 1, opt_str, long_options)) >= 0)
|
||||
{ // test command line options and apply option -x/preset first
|
||||
if (c == 'x')
|
||||
{
|
||||
if (mm_set_opt(o.arg, &ipt, &opt) < 0)
|
||||
{
|
||||
fprintf(stderr, "[ERROR] unknown preset '%s'\n", o.arg);
|
||||
return 1;
|
||||
}
|
||||
} else if (c == ':') {
|
||||
}
|
||||
else if (c == ':')
|
||||
{
|
||||
fprintf(stderr, "[ERROR] missing option argument\n");
|
||||
return 1;
|
||||
} else if (c == '?') {
|
||||
}
|
||||
else if (c == '?')
|
||||
{
|
||||
fprintf(stderr, "[ERROR] unknown option in \"%s\"\n", argv[o.i - 1]);
|
||||
return 1;
|
||||
}
|
||||
}
|
||||
o = KETOPT_INIT;
|
||||
|
||||
while ((c = ketopt(&o, argc, argv, 1, opt_str, long_options)) >= 0) {
|
||||
if (c == 'w') ipt.w = atoi(o.arg);
|
||||
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 == '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);
|
||||
else if (c == 'G') mm_mapopt_max_intron_len(&opt, (int)mm_parse_num(o.arg));
|
||||
else if (c == 'F') opt.max_frag_len = (int)mm_parse_num(o.arg);
|
||||
else if (c == 'N') old_best_n = opt.best_n, opt.best_n = atoi(o.arg);
|
||||
else if (c == 'p') opt.pri_ratio = atof(o.arg);
|
||||
else if (c == 'M') opt.mask_level = atof(o.arg);
|
||||
else if (c == 'c') opt.flag |= MM_F_OUT_CG | MM_F_CIGAR;
|
||||
else if (c == 'D') opt.flag |= MM_F_NO_DIAG;
|
||||
else if (c == 'P') opt.flag |= MM_F_ALL_CHAINS;
|
||||
else if (c == 'X') opt.flag |= MM_F_ALL_CHAINS | MM_F_NO_DIAG | MM_F_NO_DUAL | MM_F_NO_LJOIN; // -D -P --no-long-join --dual=no
|
||||
else if (c == 'a') opt.flag |= MM_F_OUT_SAM | MM_F_CIGAR;
|
||||
else if (c == 'Q') opt.flag |= MM_F_NO_QUAL;
|
||||
else if (c == 'Y') opt.flag |= MM_F_SOFTCLIP;
|
||||
else if (c == 'L') opt.flag |= MM_F_LONG_CIGAR;
|
||||
else if (c == 'y') opt.flag |= MM_F_COPY_COMMENT;
|
||||
else if (c == 'T') opt.sdust_thres = atoi(o.arg);
|
||||
else if (c == 'n') opt.min_cnt = atoi(o.arg);
|
||||
else if (c == 'm') opt.min_chain_score = atoi(o.arg);
|
||||
else if (c == 'A') opt.a = atoi(o.arg);
|
||||
else if (c == 'B') opt.b = atoi(o.arg);
|
||||
else if (c == 'b') opt.transition = atoi(o.arg);
|
||||
else if (c == 's') opt.min_dp_max = atoi(o.arg);
|
||||
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;
|
||||
else if (c == 'J') {
|
||||
while ((c = ketopt(&o, argc, argv, 1, opt_str, long_options)) >= 0)
|
||||
{
|
||||
if (c == 'w')
|
||||
ipt.w = atoi(o.arg);
|
||||
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 == '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);
|
||||
else if (c == 'G')
|
||||
mm_mapopt_max_intron_len(&opt, (int)mm_parse_num(o.arg));
|
||||
else if (c == 'F')
|
||||
opt.max_frag_len = (int)mm_parse_num(o.arg);
|
||||
else if (c == 'N')
|
||||
old_best_n = opt.best_n, opt.best_n = atoi(o.arg);
|
||||
else if (c == 'p')
|
||||
opt.pri_ratio = atof(o.arg);
|
||||
else if (c == 'M')
|
||||
opt.mask_level = atof(o.arg);
|
||||
else if (c == 'c')
|
||||
opt.flag |= MM_F_OUT_CG | MM_F_CIGAR;
|
||||
else if (c == 'D')
|
||||
opt.flag |= MM_F_NO_DIAG;
|
||||
else if (c == 'P')
|
||||
opt.flag |= MM_F_ALL_CHAINS;
|
||||
else if (c == 'X')
|
||||
opt.flag |= MM_F_ALL_CHAINS | MM_F_NO_DIAG | MM_F_NO_DUAL | MM_F_NO_LJOIN; // -D -P --no-long-join --dual=no
|
||||
else if (c == 'a')
|
||||
opt.flag |= MM_F_OUT_SAM | MM_F_CIGAR;
|
||||
else if (c == 'Q')
|
||||
opt.flag |= MM_F_NO_QUAL;
|
||||
else if (c == 'Y')
|
||||
opt.flag |= MM_F_SOFTCLIP;
|
||||
else if (c == 'L')
|
||||
opt.flag |= MM_F_LONG_CIGAR;
|
||||
else if (c == 'y')
|
||||
opt.flag |= MM_F_COPY_COMMENT;
|
||||
else if (c == 'T')
|
||||
opt.sdust_thres = atoi(o.arg);
|
||||
else if (c == 'n')
|
||||
opt.min_cnt = atoi(o.arg);
|
||||
else if (c == 'm')
|
||||
opt.min_chain_score = atoi(o.arg);
|
||||
else if (c == 'A')
|
||||
opt.a = atoi(o.arg);
|
||||
else if (c == 'B')
|
||||
opt.b = atoi(o.arg);
|
||||
else if (c == 'b')
|
||||
opt.transition = atoi(o.arg);
|
||||
else if (c == 's')
|
||||
opt.min_dp_max = atoi(o.arg);
|
||||
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;
|
||||
else if (c == 'J')
|
||||
{
|
||||
int t;
|
||||
t = atoi(o.arg);
|
||||
if (t == 0) opt.flag |= MM_F_SPLICE_OLD;
|
||||
else if (t == 1) opt.flag &= ~MM_F_SPLICE_OLD;
|
||||
} else if (c == 'o') {
|
||||
if (strcmp(o.arg, "-") != 0) {
|
||||
if (freopen(o.arg, "wb", stdout) == NULL) {
|
||||
if (t == 0)
|
||||
opt.flag |= MM_F_SPLICE_OLD;
|
||||
else if (t == 1)
|
||||
opt.flag &= ~MM_F_SPLICE_OLD;
|
||||
}
|
||||
else if (c == 'o')
|
||||
{
|
||||
if (strcmp(o.arg, "-") != 0)
|
||||
{
|
||||
if (freopen(o.arg, "wb", stdout) == NULL)
|
||||
{
|
||||
fprintf(stderr, "[ERROR]\033[1;31m failed to write the output to file '%s'\033[0m: %s\n", o.arg, strerror(errno));
|
||||
exit(1);
|
||||
}
|
||||
}
|
||||
}
|
||||
else if (c == 300) ipt.bucket_bits = atoi(o.arg); // --bucket-bits
|
||||
else if (c == 302) opt.seed = atoi(o.arg); // --seed
|
||||
else if (c == 303) mm_dbg_flag |= MM_DBG_NO_KALLOC; // --no-kalloc
|
||||
else if (c == 304) mm_dbg_flag |= MM_DBG_PRINT_QNAME; // --print-qname
|
||||
else if (c == 306) mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_SEED, n_threads = 1; // --print-seed
|
||||
else if (c == 307) opt.max_chain_skip = atoi(o.arg); // --max-chain-skip
|
||||
else if (c == 339) opt.max_chain_iter = atoi(o.arg); // --max-chain-iter
|
||||
else if (c == 308) opt.min_ksw_len = atoi(o.arg); // --min-dp-len
|
||||
else if (c == 309) mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_ALN_SEQ, n_threads = 1; // --print-aln-seq
|
||||
else if (c == 310) opt.flag |= MM_F_SPLICE; // --splice
|
||||
else if (c == 312) opt.flag |= MM_F_NO_LJOIN; // --no-long-join
|
||||
else if (c == 313) opt.flag |= MM_F_SR; // --sr
|
||||
else if (c == 317) opt.end_bonus = atoi(o.arg); // --end-bonus
|
||||
else if (c == 318) opt.flag |= MM_F_INDEPEND_SEG; // --no-pairing
|
||||
else if (c == 320) ipt.flag |= MM_I_NO_SEQ; // --idx-no-seq
|
||||
else if (c == 321) opt.anchor_ext_shift = atoi(o.arg); // --end-seed-pen
|
||||
else if (c == 322) opt.flag |= MM_F_FOR_ONLY; // --for-only
|
||||
else if (c == 323) opt.flag |= MM_F_REV_ONLY; // --rev-only
|
||||
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 == 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
|
||||
else if (c == 334) opt.split_prefix = o.arg; // --split-prefix
|
||||
else if (c == 335) opt.flag |= MM_F_NO_END_FLT; // --no-end-flt
|
||||
else if (c == 336) opt.flag |= MM_F_HARD_MLEVEL; // --hard-mask-level
|
||||
else if (c == 337) opt.max_sw_mat = mm_parse_num(o.arg); // --cap-sw-mat
|
||||
else if (c == 338) opt.max_qlen = mm_parse_num(o.arg); // --max-qlen
|
||||
else if (c == 340) junc_bed = o.arg; // --junc-bed
|
||||
else if (c == 341) opt.junc_bonus = atoi(o.arg); // --junc-bonus
|
||||
else if (c == 342) opt.flag |= MM_F_SAM_HIT_ONLY; // --sam-hit-only
|
||||
else if (c == 343) opt.chain_gap_scale = atof(o.arg); // --chain-gap-scale
|
||||
else if (c == 351) opt.chain_skip_scale = atof(o.arg); // --chain-skip-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.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 == 349) opt.cap_kalloc = mm_parse_num(o.arg); // --cap-kalloc
|
||||
else if (c == 350) opt.q_occ_frac = atof(o.arg); // --q-occ-frac
|
||||
else if (c == 352) mm_dbg_flag |= MM_DBG_PRINT_CHAIN; // --print-chains
|
||||
else if (c == 353) opt.flag |= MM_F_NO_HASH_NAME; // --no-hash-name
|
||||
else if (c == 354) opt.flag |= MM_F_SECONDARY_SEQ; // --secondary-seq
|
||||
else if (c == 330) {
|
||||
else if (c == 300)
|
||||
ipt.bucket_bits = atoi(o.arg); // --bucket-bits
|
||||
else if (c == 302)
|
||||
opt.seed = atoi(o.arg); // --seed
|
||||
else if (c == 303)
|
||||
mm_dbg_flag |= MM_DBG_NO_KALLOC; // --no-kalloc
|
||||
else if (c == 304)
|
||||
mm_dbg_flag |= MM_DBG_PRINT_QNAME; // --print-qname
|
||||
else if (c == 306)
|
||||
mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_SEED, n_threads = 1; // --print-seed
|
||||
else if (c == 307)
|
||||
opt.max_chain_skip = atoi(o.arg); // --max-chain-skip
|
||||
else if (c == 339)
|
||||
opt.max_chain_iter = atoi(o.arg); // --max-chain-iter
|
||||
else if (c == 308)
|
||||
opt.min_ksw_len = atoi(o.arg); // --min-dp-len
|
||||
else if (c == 309)
|
||||
mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_ALN_SEQ, n_threads = 1; // --print-aln-seq
|
||||
else if (c == 310)
|
||||
opt.flag |= MM_F_SPLICE; // --splice
|
||||
else if (c == 312)
|
||||
opt.flag |= MM_F_NO_LJOIN; // --no-long-join
|
||||
else if (c == 313)
|
||||
opt.flag |= MM_F_SR; // --sr
|
||||
else if (c == 317)
|
||||
opt.end_bonus = atoi(o.arg); // --end-bonus
|
||||
else if (c == 318)
|
||||
opt.flag |= MM_F_INDEPEND_SEG; // --no-pairing
|
||||
else if (c == 320)
|
||||
ipt.flag |= MM_I_NO_SEQ; // --idx-no-seq
|
||||
else if (c == 321)
|
||||
opt.anchor_ext_shift = atoi(o.arg); // --end-seed-pen
|
||||
else if (c == 322)
|
||||
opt.flag |= MM_F_FOR_ONLY; // --for-only
|
||||
else if (c == 323)
|
||||
opt.flag |= MM_F_REV_ONLY; // --rev-only
|
||||
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 == 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
|
||||
else if (c == 334)
|
||||
opt.split_prefix = o.arg; // --split-prefix
|
||||
else if (c == 335)
|
||||
opt.flag |= MM_F_NO_END_FLT; // --no-end-flt
|
||||
else if (c == 336)
|
||||
opt.flag |= MM_F_HARD_MLEVEL; // --hard-mask-level
|
||||
else if (c == 337)
|
||||
opt.max_sw_mat = mm_parse_num(o.arg); // --cap-sw-mat
|
||||
else if (c == 338)
|
||||
opt.max_qlen = mm_parse_num(o.arg); // --max-qlen
|
||||
else if (c == 340)
|
||||
junc_bed = o.arg; // --junc-bed
|
||||
else if (c == 341)
|
||||
opt.junc_bonus = atoi(o.arg); // --junc-bonus
|
||||
else if (c == 342)
|
||||
opt.flag |= MM_F_SAM_HIT_ONLY; // --sam-hit-only
|
||||
else if (c == 343)
|
||||
opt.chain_gap_scale = atof(o.arg); // --chain-gap-scale
|
||||
else if (c == 351)
|
||||
opt.chain_skip_scale = atof(o.arg); // --chain-skip-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.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 == 349)
|
||||
opt.cap_kalloc = mm_parse_num(o.arg); // --cap-kalloc
|
||||
else if (c == 350)
|
||||
opt.q_occ_frac = atof(o.arg); // --q-occ-frac
|
||||
else if (c == 352)
|
||||
mm_dbg_flag |= MM_DBG_PRINT_CHAIN; // --print-chains
|
||||
else if (c == 353)
|
||||
opt.flag |= MM_F_NO_HASH_NAME; // --no-hash-name
|
||||
else if (c == 354)
|
||||
opt.flag |= MM_F_SECONDARY_SEQ; // --secondary-seq
|
||||
else if (c == 330)
|
||||
{
|
||||
fprintf(stderr, "[WARNING] \033[1;31m --lj-min-ratio has been deprecated.\033[0m\n");
|
||||
} else if (c == 314) { // --frag
|
||||
}
|
||||
else if (c == 314)
|
||||
{ // --frag
|
||||
yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
|
||||
} else if (c == 315) { // --secondary
|
||||
}
|
||||
else if (c == 315)
|
||||
{ // --secondary
|
||||
yes_or_no(&opt, MM_F_NO_PRINT_2ND, o.longidx, o.arg, 0);
|
||||
} else if (c == 316) { // --cs
|
||||
}
|
||||
else if (c == 316)
|
||||
{ // --cs
|
||||
opt.flag |= MM_F_OUT_CS | MM_F_CIGAR;
|
||||
if (o.arg == 0 || strcmp(o.arg, "short") == 0) {
|
||||
if (o.arg == 0 || strcmp(o.arg, "short") == 0)
|
||||
{
|
||||
opt.flag &= ~MM_F_OUT_CS_LONG;
|
||||
} else if (strcmp(o.arg, "long") == 0) {
|
||||
}
|
||||
else if (strcmp(o.arg, "long") == 0)
|
||||
{
|
||||
opt.flag |= MM_F_OUT_CS_LONG;
|
||||
} else if (strcmp(o.arg, "none") == 0) {
|
||||
}
|
||||
else if (strcmp(o.arg, "none") == 0)
|
||||
{
|
||||
opt.flag &= ~MM_F_OUT_CS;
|
||||
} else if (mm_verbose >= 2) {
|
||||
}
|
||||
else if (mm_verbose >= 2)
|
||||
{
|
||||
fprintf(stderr, "[WARNING]\033[1;31m --cs only takes 'short' or 'long'. Invalid values are assumed to be 'short'.\033[0m\n");
|
||||
}
|
||||
} else if (c == 319) { // --splice-flank
|
||||
}
|
||||
else if (c == 319)
|
||||
{ // --splice-flank
|
||||
yes_or_no(&opt, MM_F_SPLICE_FLANK, o.longidx, o.arg, 1);
|
||||
} else if (c == 324) { // --heap-sort
|
||||
}
|
||||
else if (c == 324)
|
||||
{ // --heap-sort
|
||||
yes_or_no(&opt, MM_F_HEAP_SORT, o.longidx, o.arg, 1);
|
||||
} else if (c == 326) { // --dual
|
||||
}
|
||||
else if (c == 326)
|
||||
{ // --dual
|
||||
yes_or_no(&opt, MM_F_NO_DUAL, o.longidx, o.arg, 0);
|
||||
} else if (c == 347) { // --rmq
|
||||
if (o.arg) yes_or_no(&opt, MM_F_RMQ, o.longidx, o.arg, 1);
|
||||
else opt.flag |= MM_F_RMQ;
|
||||
} else if (c == 'S') {
|
||||
}
|
||||
else if (c == 347)
|
||||
{ // --rmq
|
||||
if (o.arg)
|
||||
yes_or_no(&opt, MM_F_RMQ, o.longidx, o.arg, 1);
|
||||
else
|
||||
opt.flag |= MM_F_RMQ;
|
||||
}
|
||||
else if (c == 'S')
|
||||
{
|
||||
opt.flag |= MM_F_OUT_CS | MM_F_CIGAR | MM_F_OUT_CS_LONG;
|
||||
if (mm_verbose >= 2)
|
||||
fprintf(stderr, "[WARNING]\033[1;31m option -S is deprecated and may be removed in future. Please use --cs=long instead.\033[0m\n");
|
||||
} else if (c == 'V') {
|
||||
}
|
||||
else if (c == 'V')
|
||||
{
|
||||
puts(MM_VERSION);
|
||||
return 0;
|
||||
} else if (c == 'r') {
|
||||
}
|
||||
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') {
|
||||
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') {
|
||||
if (*s == ',')
|
||||
opt.max_mid_occ = strtol(s + 1, &s, 10);
|
||||
}
|
||||
else if (c == 'f')
|
||||
{
|
||||
double x;
|
||||
char *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 (*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 {
|
||||
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 (*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') {
|
||||
}
|
||||
else if (c == 'z')
|
||||
{
|
||||
opt.zdrop = opt.zdrop_inv = strtol(o.arg, &s, 10);
|
||||
if (*s == ',') opt.zdrop_inv = strtol(s + 1, &s, 10);
|
||||
} else if (c == 'O') {
|
||||
if (*s == ',')
|
||||
opt.zdrop_inv = strtol(s + 1, &s, 10);
|
||||
}
|
||||
else if (c == 'O')
|
||||
{
|
||||
opt.q = opt.q2 = strtol(o.arg, &s, 10);
|
||||
if (*s == ',') opt.q2 = strtol(s + 1, &s, 10);
|
||||
} else if (c == 'E') {
|
||||
if (*s == ',')
|
||||
opt.q2 = strtol(s + 1, &s, 10);
|
||||
}
|
||||
else if (c == 'E')
|
||||
{
|
||||
opt.e = opt.e2 = strtol(o.arg, &s, 10);
|
||||
if (*s == ',') opt.e2 = strtol(s + 1, &s, 10);
|
||||
if (*s == ',')
|
||||
opt.e2 = strtol(s + 1, &s, 10);
|
||||
}
|
||||
}
|
||||
if ((opt.flag & MM_F_SPLICE) && (opt.flag & MM_F_FRAG_MODE)) {
|
||||
if ((opt.flag & MM_F_SPLICE) && (opt.flag & MM_F_FRAG_MODE))
|
||||
{
|
||||
fprintf(stderr, "[ERROR]\033[1;31m --splice and --frag should not be specified at the same time.\033[0m\n");
|
||||
return 1;
|
||||
}
|
||||
if (!fnw && !(opt.flag&MM_F_CIGAR))
|
||||
if (!fnw && !(opt.flag & MM_F_CIGAR))
|
||||
ipt.flag |= MM_I_NO_SEQ;
|
||||
if (mm_check_opt(&ipt, &opt) < 0)
|
||||
return 1;
|
||||
if (opt.best_n == 0) {
|
||||
if (opt.best_n == 0)
|
||||
{
|
||||
fprintf(stderr, "[WARNING]\033[1;31m changed '-N 0' to '-N %d --secondary=no'.\033[0m\n", old_best_n);
|
||||
opt.best_n = old_best_n, opt.flag |= MM_F_NO_PRINT_2ND;
|
||||
}
|
||||
|
||||
if (argc == o.ind || 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");
|
||||
|
|
@ -339,7 +551,7 @@ int main(int argc, char *argv[])
|
|||
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
|
||||
// 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
|
||||
fprintf(fp_help, " -X skip self and dual mappings (for the all-vs-all mode)\n");
|
||||
fprintf(fp_help, " -p FLOAT min secondary-to-primary score ratio [%g]\n", opt.pri_ratio);
|
||||
fprintf(fp_help, " -N INT retain at most INT secondary alignments [%d]\n", opt.best_n);
|
||||
|
|
@ -364,7 +576,7 @@ int main(int argc, char *argv[])
|
|||
fprintf(fp_help, " -Y use soft clipping for supplementary alignments\n");
|
||||
fprintf(fp_help, " -t INT number of threads [%d]\n", n_threads);
|
||||
fprintf(fp_help, " -K NUM minibatch size for mapping [500M]\n");
|
||||
// fprintf(fp_help, " -v INT verbose level [%d]\n", mm_verbose);
|
||||
// fprintf(fp_help, " -v INT verbose level [%d]\n", mm_verbose);
|
||||
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");
|
||||
|
|
@ -375,45 +587,55 @@ int main(int argc, char *argv[])
|
|||
fprintf(fp_help, " - splice/splice:hq - long-read/Pacbio-CCS spliced alignment\n");
|
||||
fprintf(fp_help, " - sr - genomic short-read mapping\n");
|
||||
fprintf(fp_help, "\nSee `man ./minimap2.1' for detailed description of these and other advanced command-line options.\n");
|
||||
return fp_help == stdout? 0 : 1;
|
||||
return fp_help == stdout ? 0 : 1;
|
||||
}
|
||||
|
||||
if ((opt.flag & MM_F_SR) && argc - o.ind > 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[o.ind], &ipt, fnw);
|
||||
if (idx_rdr == 0) {
|
||||
if (idx_rdr == 0)
|
||||
{
|
||||
fprintf(stderr, "[ERROR] failed to open file '%s': %s\n", argv[o.ind], strerror(errno));
|
||||
return 1;
|
||||
}
|
||||
if (!idx_rdr->is_idx && fnw == 0 && argc - o.ind < 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;
|
||||
}
|
||||
if (opt.best_n == 0 && (opt.flag&MM_F_CIGAR) && mm_verbose >= 2)
|
||||
if (opt.best_n == 0 && (opt.flag & MM_F_CIGAR) && mm_verbose >= 2)
|
||||
fprintf(stderr, "[WARNING]\033[1;31m `-N 0' reduces alignment accuracy. Please use --secondary=no to suppress secondary alignments.\033[0m\n");
|
||||
while ((mi = mm_idx_reader_read(idx_rdr, n_threads)) != 0) {
|
||||
while ((mi = mm_idx_reader_read(idx_rdr, n_threads)) != 0)
|
||||
{
|
||||
int ret;
|
||||
if ((opt.flag & MM_F_CIGAR) && (mi->flag & MM_I_NO_SEQ)) {
|
||||
if ((opt.flag & MM_F_CIGAR) && (mi->flag & MM_I_NO_SEQ))
|
||||
{
|
||||
fprintf(stderr, "[ERROR] the prebuilt index doesn't contain sequences.\n");
|
||||
mm_idx_destroy(mi);
|
||||
mm_idx_reader_close(idx_rdr);
|
||||
return 1;
|
||||
}
|
||||
if ((opt.flag & MM_F_OUT_SAM) && idx_rdr->n_parts == 1) {
|
||||
if (mm_idx_reader_eof(idx_rdr)) {
|
||||
if ((opt.flag & MM_F_OUT_SAM) && idx_rdr->n_parts == 1)
|
||||
{
|
||||
if (mm_idx_reader_eof(idx_rdr))
|
||||
{
|
||||
if (opt.split_prefix == 0)
|
||||
ret = mm_write_sam_hdr(mi, rg, MM_VERSION, argc, argv);
|
||||
else
|
||||
ret = mm_write_sam_hdr(0, rg, MM_VERSION, argc, argv);
|
||||
} else {
|
||||
}
|
||||
else
|
||||
{
|
||||
ret = mm_write_sam_hdr(0, rg, MM_VERSION, argc, argv);
|
||||
if (opt.split_prefix == 0 && mm_verbose >= 2)
|
||||
fprintf(stderr, "[WARNING]\033[1;31m For a multi-part index, no @SQ lines will be outputted. Please use --split-prefix.\033[0m\n");
|
||||
}
|
||||
if (ret != 0) {
|
||||
if (ret != 0)
|
||||
{
|
||||
mm_idx_destroy(mi);
|
||||
mm_idx_reader_close(idx_rdr);
|
||||
return 1;
|
||||
|
|
@ -422,25 +644,37 @@ 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 != o.ind + 1) mm_mapopt_update(&opt, mi);
|
||||
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) {
|
||||
if (argc != o.ind + 1)
|
||||
mm_mapopt_update(&opt, mi);
|
||||
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)
|
||||
{
|
||||
mm_idx_destroy(mi);
|
||||
continue; // no query files
|
||||
}
|
||||
ret = 0;
|
||||
if (!(opt.flag & MM_F_FRAG_MODE)) {
|
||||
for (i = o.ind + 1; i < argc; ++i) {
|
||||
if (!(opt.flag & MM_F_FRAG_MODE))
|
||||
{
|
||||
// 如果是read / read overlap操作，那么把第一个输入的read.fq当做索引，后续的read比对到该索引
|
||||
for (i = o.ind + 1; i < argc; ++i)
|
||||
{
|
||||
ret = mm_map_file(mi, argv[i], &opt, n_threads);
|
||||
if (ret < 0) break;
|
||||
if (ret < 0)
|
||||
break;
|
||||
}
|
||||
} else {
|
||||
ret = mm_map_file_frag(mi, argc - (o.ind + 1), (const char**)&argv[o.ind + 1], &opt, n_threads);
|
||||
}
|
||||
else
|
||||
{
|
||||
ret = mm_map_file_frag(mi, argc - (o.ind + 1), (const char **)&argv[o.ind + 1], &opt, n_threads);
|
||||
}
|
||||
mm_idx_destroy(mi);
|
||||
if (ret < 0) {
|
||||
if (ret < 0)
|
||||
{
|
||||
fprintf(stderr, "ERROR: failed to map the query file\n");
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
|
@ -449,19 +683,42 @@ int main(int argc, char *argv[])
|
|||
mm_idx_reader_close(idx_rdr);
|
||||
|
||||
if (opt.split_prefix)
|
||||
mm_split_merge(argc - (o.ind + 1), (const char**)&argv[o.ind + 1], &opt, n_parts);
|
||||
mm_split_merge(argc - (o.ind + 1), (const char **)&argv[o.ind + 1], &opt, n_parts);
|
||||
|
||||
if (fflush(stdout) == EOF) {
|
||||
if (fflush(stdout) == EOF)
|
||||
{
|
||||
perror("[ERROR] failed to write the results");
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
if (mm_verbose >= 3) {
|
||||
if (mm_verbose >= 3)
|
||||
{
|
||||
fprintf(stderr, "[M::%s] Version: %s\n", __func__, MM_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__, realtime() - mm_realtime0, cputime(), peakrss() / 1024.0 / 1024.0 / 1024.0);
|
||||
}
|
||||
#ifdef ANALYSIS_PERF
|
||||
fprintf(stderr, "\n");
|
||||
|
||||
fprintf(stderr, "time_mm_idx_reader_read: %f s\n", time_mm_idx_reader_read / 1000.0);
|
||||
fprintf(stderr, "time_mm_map_file_frag: %f s\n", time_mm_map_file_frag / 1000.0);
|
||||
fprintf(stderr, "time_map_work_for_block_1: %f s\n", time_map_work_for_block_1 / 1000.0 / n_threads);
|
||||
fprintf(stderr, "time_map_work_for_block_2: %f s\n", time_map_work_for_block_2 / 1000.0 / n_threads);
|
||||
fprintf(stderr, "time_map_work_for_block_3: %f s\n", time_map_work_for_block_3 / 1000.0 / n_threads);
|
||||
fprintf(stderr, "time_mm_map_frag_b1: %f s\n", time_mm_map_frag_b1 / 1000.0 / n_threads);
|
||||
fprintf(stderr, "time_mm_map_frag_b2: %f s\n", time_mm_map_frag_b2 / 1000.0 / n_threads);
|
||||
fprintf(stderr, "time_mm_map_frag_b3: %f s\n", time_mm_map_frag_b3 / 1000.0 / n_threads);
|
||||
fprintf(stderr, "time_mm_map_frag_b4: %f s\n", time_mm_map_frag_b4 / 1000.0 / n_threads);
|
||||
fprintf(stderr, "time_mm_map_frag_b5: %f s\n", time_mm_map_frag_b5 / 1000.0 / n_threads);
|
||||
fprintf(stderr, "time_mm_map_frag_b6: %f s\n", time_mm_map_frag_b6 / 1000.0 / n_threads);
|
||||
fprintf(stderr, "time_collect_seed_hits_heap: %f s\n", time_collect_seed_hits_heap / 1000.0 / n_threads);
|
||||
fprintf(stderr, "time_collect_seed_hits: %f s\n", time_collect_seed_hits / 1000.0 / n_threads);
|
||||
fprintf(stderr, "time_mg_lchain_dp: %f s\n", time_mg_lchain_dp / 1000.0 / n_threads);
|
||||
fprintf(stderr, "time_mg_chain_backtrack: %f s\n", time_mg_chain_backtrack / 1000.0 / n_threads);
|
||||
|
||||
fprintf(stderr, "\n");
|
||||
#endif
|
||||
return 0;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -7,6 +7,9 @@
|
|||
|
||||
#define MM_VERSION "2.26-r1175"
|
||||
|
||||
// 用来开关调试性能分析，运行时间等信息
|
||||
#define ANALYSIS_PERF 1
|
||||
|
||||
#define MM_F_NO_DIAG (0x001LL) // no exact diagonal hit
|
||||
#define MM_F_NO_DUAL (0x002LL) // skip pairs where query name is lexicographically larger than target name
|
||||
#define MM_F_CIGAR (0x004LL)
|
||||
|
|
|
|||
2
sketch.c
2
sketch.c
|
|
@ -106,7 +106,7 @@ void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, i
|
|||
kmer[0] = (kmer[0] << 2 | c) & mask; // forward k-mer
|
||||
kmer[1] = (kmer[1] >> 2) | (3ULL^c) << shift1; // reverse k-mer
|
||||
if (kmer[0] == kmer[1]) continue; // skip "symmetric k-mers" as we don't know it strand
|
||||
z = kmer[0] < kmer[1]? 0 : 1; // strand
|
||||
z = kmer[0] < kmer[1]? 0 : 1; // strand // kmer的strand到底是什么意思？为什么通过比较就能确定正反？
|
||||
++l;
|
||||
if (l >= k && kmer_span < 256) {
|
||||
info.x = hash64(kmer[z], mask) << 8 | kmer_span;
|
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|
|
|
|||
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Reference in New Issue