diff --git a/format.c b/format.c index 144005a..2d3af37 100644 --- a/format.c +++ b/format.c @@ -6,6 +6,8 @@ #include "kalloc.h" #include "mmpriv.h" +static char *mm_rg_line, mm_rg_id[256]; + static inline void str_enlarge(kstring_t *s, int l) { if (s->l + l + 1 > s->m) { @@ -56,6 +58,60 @@ static void mm_sprintf_lite(kstring_t *s, const char *fmt, ...) s->s[s->l] = 0; } +static inline char *mm_escape(char *s) +{ + char *p, *q; + for (p = q = s; *p; ++p) { + if (*p == '\\') { + ++p; + if (*p == 't') *q++ = '\t'; + else if (*p == 'n') *q++ = '\n'; + else if (*p == 'r') *q++ = '\r'; + else if (*p == '\\') *q++ = '\\'; + } else *q++ = *p; + } + *q = '\0'; + return s; +} + +void mm_set_rg(const char *s) +{ + char *p, *q, *r, *rg_line = 0; + memset(mm_rg_id, 0, 256); + if (mm_rg_line) { + free(mm_rg_line); + mm_rg_line = 0; + } + if (s == 0) return; + if (strstr(s, "@RG") != s) { + if (mm_verbose >= 1) fprintf(stderr, "[E::%s] the read group line is not started with @RG\n", __func__); + goto err_set_rg; + } + if (strstr(s, "\t") != NULL) { + if (mm_verbose >= 1) fprintf(stderr, "[E::%s] the read group line contained literal characters -- replace with escaped tabs: \\t\n", __func__); + goto err_set_rg; + } + rg_line = strdup(s); + mm_escape(rg_line); + if ((p = strstr(rg_line, "\tID:")) == 0) { + if (mm_verbose >= 1) fprintf(stderr, "[E::%s] no ID within the read group line\n", __func__); + goto err_set_rg; + } + p += 4; + for (q = p; *q && *q != '\t' && *q != '\n'; ++q); + if (q - p + 1 > 256) { + if (mm_verbose >= 1) fprintf(stderr, "[E::%s] @RG:ID is longer than 255 characters\n", __func__); + goto err_set_rg; + } + for (q = p, r = mm_rg_id; *q && *q != '\t' && *q != '\n'; ++q) + *r++ = *q; + mm_rg_line = rg_line; + return; + +err_set_rg: + free(rg_line); +} + static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r) { extern unsigned char seq_nt4_table[256]; @@ -162,6 +218,14 @@ static char comp_tab[] = { 'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', 123, 124, 125, 126, 127 }; +void sam_write_sam_header(const mm_idx_t *idx) +{ + uint32_t i; + for (i = 0; i < idx->n_seq; ++i) + printf("@SQ\tSN:%s\tLN:%d\n", idx->seq[i].name, idx->seq[i].len); + if (mm_rg_line) puts(mm_rg_line); +} + static void sam_write_sq(kstring_t *s, char *seq, int l, int rev, int comp) { if (rev) { @@ -218,6 +282,8 @@ void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m else mm_sprintf_lite(s, "*"); } write_tags(s, r); + if (mm_rg_line && mm_rg_id[0]) + mm_sprintf_lite(s, "\tRG:Z:%s", mm_rg_id); if (r->parent == r->id && r->p && n_regs > 1 && regs && r >= regs && r - regs < n_regs) { // supplementary aln may exist int i, n_sa = 0; // n_sa: number of SA fields for (i = 0; i < n_regs; ++i) diff --git a/main.c b/main.c index 6a084fb..d526a44 100644 --- a/main.c +++ b/main.c @@ -33,6 +33,7 @@ static struct option long_options[] = { { "print-aln-seq", no_argument, 0, 0 }, { "splice", no_argument, 0, 0 }, { "cost-non-gt-ag", required_argument, 0, 0 }, + { "help", no_argument, 0, 'h' }, { "max-intron-len", required_argument, 0, 'G' }, { "version", no_argument, 0, 'V' }, { "min-count", required_argument, 0, 'n' }, @@ -62,13 +63,13 @@ int main(int argc, char *argv[]) uint64_t batch_size = 4000000000ULL; mm_bseq_file_t *fp = 0; char *fnw = 0, *s; - FILE *fpr = 0, *fpw = 0; + FILE *fpr = 0, *fpw = 0, *fp_help = stderr; liftrlimit(); mm_realtime0 = realtime(); mm_mapopt_init(&opt); - while ((c = getopt_long(argc, argv, "aSw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:", long_options, &long_idx)) >= 0) { + while ((c = getopt_long(argc, argv, "aSw: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:h", long_options, &long_idx)) >= 0) { if (c == 'w') w = atoi(optarg), idx_par_set = 1; else if (c == 'k') k = atoi(optarg), idx_par_set = 1; else if (c == 'H') is_hpc = 1, idx_par_set = 1; @@ -96,6 +97,8 @@ int main(int argc, char *argv[]) else if (c == 's') opt.min_dp_max = atoi(optarg); else if (c == 'I') batch_size = mm_parse_num(optarg); else if (c == 'K') minibatch_size = (int)mm_parse_num(optarg); + else if (c == 'R') mm_set_rg(optarg); // WARNING: this modifies global variables in format.c + else if (c == 'h') fp_help = stdout; else if (c == 0 && long_idx == 0) bucket_bits = atoi(optarg); // --bucket-bits else if (c == 0 && long_idx == 2) keep_name = 0; // --int-rname else if (c == 0 && long_idx == 3) mm_dbg_flag |= MM_DBG_NO_KALLOC; // --no-kalloc @@ -166,54 +169,55 @@ int main(int argc, char *argv[]) if ((opt.flag & MM_F_SPLICE) && max_intron_len > 0) opt.max_gap_ref = opt.bw = max_intron_len; - if (argc == optind) { - fprintf(stderr, "Usage: minimap2 [options] | [query.fa] [...]\n"); - fprintf(stderr, "Options:\n"); - fprintf(stderr, " Indexing:\n"); - fprintf(stderr, " -H use homopolymer-compressed k-mer\n"); - fprintf(stderr, " -k INT k-mer size (no larger than 28) [%d]\n", k); - fprintf(stderr, " -w INT minizer window size [{-k}*2/3]\n"); - fprintf(stderr, " -I NUM split index for every ~NUM input bases [4G]\n"); - fprintf(stderr, " -d FILE dump index to FILE []\n"); - fprintf(stderr, " Mapping:\n"); - fprintf(stderr, " -f FLOAT filter out top FLOAT fraction of repetitive minimizers [%g]\n", opt.mid_occ_frac); - fprintf(stderr, " -g INT stop chain enlongation if there are no minimizers in INT-bp [%d]\n", opt.max_gap); - fprintf(stderr, " -r INT bandwidth used in chaining and DP-based alignment [%d]\n", opt.bw); - fprintf(stderr, " -n INT minimal number of minimizers on a chain [%d]\n", opt.min_cnt); - fprintf(stderr, " -m INT minimal chaining score (matching bases minus log gap penalty) [%d]\n", opt.min_chain_score); -// fprintf(stderr, " -T INT SDUST threshold; 0 to disable SDUST [%d]\n", opt.sdust_thres); // TODO: this option is never used; might be buggy - fprintf(stderr, " -X skip self and dual mappings (for the all-vs-all mode)\n"); - fprintf(stderr, " -p FLOAT min secondary-to-primary score ratio [%g]\n", opt.pri_ratio); - fprintf(stderr, " -N INT retain at most INT secondary alignments [%d]\n", opt.best_n); - fprintf(stderr, " -G NUM max intron length (only effective following -x splice) [200k]\n"); - fprintf(stderr, " Alignment:\n"); - fprintf(stderr, " -A INT matching score [%d]\n", opt.a); - fprintf(stderr, " -B INT mismatch penalty [%d]\n", opt.b); - fprintf(stderr, " -O INT[,INT] gap open penalty [%d,%d]\n", opt.q, opt.q2); - fprintf(stderr, " -E INT[,INT] gap extension penalty; a k-long gap costs min{O1+k*E1,O2+k*E2} [%d,%d]\n", opt.e, opt.e2); - fprintf(stderr, " -z INT Z-drop score [%d]\n", opt.zdrop); - fprintf(stderr, " -s INT minimal peak DP alignment score [%d]\n", opt.min_dp_max); - fprintf(stderr, " -u CHAR how to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG [n]\n"); - fprintf(stderr, " Input/Output:\n"); - fprintf(stderr, " -Q ignore base quality in the input\n"); - fprintf(stderr, " -a output in the SAM format (PAF by default)\n"); - fprintf(stderr, " -c output CIGAR in PAF\n"); - fprintf(stderr, " -S output the cs tag in PAF\n"); - fprintf(stderr, " -t INT number of threads [%d]\n", n_threads); - fprintf(stderr, " -K NUM minibatch size [200M]\n"); -// fprintf(stderr, " -v INT verbose level [%d]\n", mm_verbose); - fprintf(stderr, " -V show version number\n"); - fprintf(stderr, " Preset:\n"); - fprintf(stderr, " -x STR preset (recommended to be applied before other options) []\n"); - fprintf(stderr, " map10k/map-pb: -Hk19 (PacBio/ONT vs reference mapping)\n"); - fprintf(stderr, " map-ont: -k15 (slightly more sensitive than 'map10k' for ONT vs reference)\n"); - fprintf(stderr, " asm5: -k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 (asm to ref mapping; break at 5%% div.)\n"); - fprintf(stderr, " asm10: -k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 (asm to ref mapping; break at 10%% div.)\n"); - fprintf(stderr, " ava-pb: -Hk19 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (PacBio read overlap)\n"); - fprintf(stderr, " ava-ont: -k15 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (ONT read overlap)\n"); - fprintf(stderr, " splice: long-read spliced alignment (see minimap2.1 for details)\n"); - fprintf(stderr, "\nSee `man ./minimap2.1' for detailed description of command-line options.\n"); - return 1; + if (argc == optind || fp_help == stdout) { + fprintf(fp_help, "Usage: minimap2 [options] | [query.fa] [...]\n"); + fprintf(fp_help, "Options:\n"); + fprintf(fp_help, " Indexing:\n"); + fprintf(fp_help, " -H use homopolymer-compressed k-mer\n"); + fprintf(fp_help, " -k INT k-mer size (no larger than 28) [%d]\n", k); + fprintf(fp_help, " -w INT minizer window size [{-k}*2/3]\n"); + fprintf(fp_help, " -I NUM split index for every ~NUM input bases [4G]\n"); + fprintf(fp_help, " -d FILE dump index to FILE []\n"); + fprintf(fp_help, " Mapping:\n"); + fprintf(fp_help, " -f FLOAT filter out top FLOAT fraction of repetitive minimizers [%g]\n", opt.mid_occ_frac); + fprintf(fp_help, " -g INT stop chain enlongation if there are no minimizers in INT-bp [%d]\n", opt.max_gap); + fprintf(fp_help, " -r INT bandwidth used in chaining and DP-based alignment [%d]\n", opt.bw); + 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, " -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); + fprintf(fp_help, " -G NUM max intron length (only effective following -x splice) [200k]\n"); + fprintf(fp_help, " Alignment:\n"); + fprintf(fp_help, " -A INT matching score [%d]\n", opt.a); + fprintf(fp_help, " -B INT mismatch penalty [%d]\n", opt.b); + fprintf(fp_help, " -O INT[,INT] gap open penalty [%d,%d]\n", opt.q, opt.q2); + fprintf(fp_help, " -E INT[,INT] gap extension penalty; a k-long gap costs min{O1+k*E1,O2+k*E2} [%d,%d]\n", opt.e, opt.e2); + fprintf(fp_help, " -z INT Z-drop score [%d]\n", opt.zdrop); + fprintf(fp_help, " -s INT minimal peak DP alignment score [%d]\n", opt.min_dp_max); + fprintf(fp_help, " -u CHAR how to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG [n]\n"); + fprintf(fp_help, " Input/Output:\n"); + fprintf(fp_help, " -a output in the SAM format (PAF by default)\n"); + fprintf(fp_help, " -Q don't output base quality in SAM\n"); + fprintf(fp_help, " -R STR SAM read group line in a format like '@RG\\tID:foo\\tSM:bar' []\n"); + fprintf(fp_help, " -c output CIGAR in PAF\n"); + fprintf(fp_help, " -S output the cs tag in PAF (cs encodes both query and ref sequences)\n"); + fprintf(fp_help, " -t INT number of threads [%d]\n", n_threads); + fprintf(fp_help, " -K NUM minibatch size [200M]\n"); +// 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 (recommended to be applied before other options) []\n"); + fprintf(fp_help, " map10k/map-pb: -Hk19 (PacBio/ONT vs reference mapping)\n"); + fprintf(fp_help, " map-ont: -k15 (slightly more sensitive than 'map10k' for ONT vs reference)\n"); + fprintf(fp_help, " asm5: -k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 (asm to ref mapping; break at 5%% div.)\n"); + fprintf(fp_help, " asm10: -k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 (asm to ref mapping; break at 10%% div.)\n"); + fprintf(fp_help, " ava-pb: -Hk19 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (PacBio read overlap)\n"); + fprintf(fp_help, " ava-ont: -k15 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (ONT read overlap)\n"); + fprintf(fp_help, " splice: long-read spliced alignment (see minimap2.1 for details)\n"); + fprintf(fp_help, "\nSee `man ./minimap2.1' for detailed description of command-line options.\n"); + return fp_help == stdout? 0 : 1; } is_idx = mm_idx_is_idx(argv[optind]); diff --git a/map.c b/map.c index f8654b2..630c78a 100644 --- a/map.c +++ b/map.c @@ -388,11 +388,7 @@ int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int if (pl.fp == 0) return -1; pl.opt = opt, pl.mi = idx; pl.n_threads = n_threads, pl.mini_batch_size = mini_batch_size; - if (opt->flag & MM_F_OUT_SAM) { - uint32_t i; - for (i = 0; i < idx->n_seq; ++i) - printf("@SQ\tSN:%s\tLN:%d\n", idx->seq[i].name, idx->seq[i].len); - } + if (opt->flag & MM_F_OUT_SAM) sam_write_sam_header(idx); kt_pipeline(n_threads == 1? 1 : 2, worker_pipeline, &pl, 3); free(pl.str.s); mm_bseq_close(pl.fp); diff --git a/minimap2.1 b/minimap2.1 index 5b8aee3..d2d2530 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -219,13 +219,18 @@ no attempt to match GT-AG [n] Cost of non-canonical splicing sites [0]. .SS Input/output options .TP 10 -.B -Q -Ignore base quality in the input file. -.TP .B -a Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF by default. .TP +.B -Q +Ignore base quality in the input file. +.TP +.BI -R \ STR +SAM read group line in a format like +.B @RG\\\\tID:foo\\\\tSM:bar +[]. +.TP .B -c Generate CIGAR. In PAF, the CIGAR is written to the `cg' custom tag. .TP diff --git a/mmpriv.h b/mmpriv.h index 83cfcf4..becf5e4 100644 --- a/mmpriv.h +++ b/mmpriv.h @@ -40,6 +40,8 @@ void radix_sort_128x(mm128_t *beg, mm128_t *end); void radix_sort_64(uint64_t *beg, uint64_t *end); uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk); +void mm_set_rg(const char *s); +void sam_write_sam_header(const mm_idx_t *idx); void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag, int intron_thres); void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int n_regs, const mm_reg1_t *regs, int intron_thres); int mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int min_cnt, int min_sc, int is_cdna, int64_t n, mm128_t *a, uint64_t **_u, void *km);