support inserting RG lines
This commit is contained in:
Heng Li
parent
b5f5929bf9
commit
bbb37d95f2
66
format.c
66
format.c
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@ -6,6 +6,8 @@
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#include "kalloc.h"
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#include "mmpriv.h"
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static char *mm_rg_line, mm_rg_id[256];
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static inline void str_enlarge(kstring_t *s, int l)
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{
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if (s->l + l + 1 > s->m) {
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@ -56,6 +58,60 @@ static void mm_sprintf_lite(kstring_t *s, const char *fmt, ...)
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s->s[s->l] = 0;
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}
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static inline char *mm_escape(char *s)
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{
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char *p, *q;
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for (p = q = s; *p; ++p) {
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if (*p == '\\') {
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++p;
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if (*p == 't') *q++ = '\t';
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else if (*p == 'n') *q++ = '\n';
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else if (*p == 'r') *q++ = '\r';
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else if (*p == '\\') *q++ = '\\';
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} else *q++ = *p;
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}
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*q = '\0';
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return s;
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}
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void mm_set_rg(const char *s)
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{
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char *p, *q, *r, *rg_line = 0;
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memset(mm_rg_id, 0, 256);
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if (mm_rg_line) {
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free(mm_rg_line);
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mm_rg_line = 0;
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}
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if (s == 0) return;
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if (strstr(s, "@RG") != s) {
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if (mm_verbose >= 1) fprintf(stderr, "[E::%s] the read group line is not started with @RG\n", __func__);
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goto err_set_rg;
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}
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if (strstr(s, "\t") != NULL) {
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if (mm_verbose >= 1) fprintf(stderr, "[E::%s] the read group line contained literal <tab> characters -- replace with escaped tabs: \\t\n", __func__);
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goto err_set_rg;
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}
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rg_line = strdup(s);
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mm_escape(rg_line);
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if ((p = strstr(rg_line, "\tID:")) == 0) {
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if (mm_verbose >= 1) fprintf(stderr, "[E::%s] no ID within the read group line\n", __func__);
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goto err_set_rg;
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}
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p += 4;
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for (q = p; *q && *q != '\t' && *q != '\n'; ++q);
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if (q - p + 1 > 256) {
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if (mm_verbose >= 1) fprintf(stderr, "[E::%s] @RG:ID is longer than 255 characters\n", __func__);
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goto err_set_rg;
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}
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for (q = p, r = mm_rg_id; *q && *q != '\t' && *q != '\n'; ++q)
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*r++ = *q;
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mm_rg_line = rg_line;
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return;
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err_set_rg:
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free(rg_line);
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}
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static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r)
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{
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extern unsigned char seq_nt4_table[256];
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@ -158,6 +214,14 @@ static char comp_tab[] = {
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'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', 123, 124, 125, 126, 127
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};
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void sam_write_sam_header(const mm_idx_t *idx)
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{
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uint32_t i;
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for (i = 0; i < idx->n_seq; ++i)
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printf("@SQ\tSN:%s\tLN:%d\n", idx->seq[i].name, idx->seq[i].len);
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if (mm_rg_line) puts(mm_rg_line);
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}
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static void sam_write_sq(kstring_t *s, char *seq, int l, int rev, int comp)
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{
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if (rev) {
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@ -214,6 +278,8 @@ void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
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else mm_sprintf_lite(s, "*");
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}
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write_tags(s, r);
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if (mm_rg_line && mm_rg_id[0])
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mm_sprintf_lite(s, "\tRG:Z:%s", mm_rg_id);
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if (r->parent == r->id && r->p && n_regs > 1 && regs && r >= regs && r - regs < n_regs) { // supplementary aln may exist
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int i, n_sa = 0; // n_sa: number of SA fields
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for (i = 0; i < n_regs; ++i)
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10
main.c
10
main.c
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@ -68,7 +68,7 @@ int main(int argc, char *argv[])
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mm_realtime0 = realtime();
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mm_mapopt_init(&opt);
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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) {
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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:", long_options, &long_idx)) >= 0) {
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if (c == 'w') w = atoi(optarg), idx_par_set = 1;
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else if (c == 'k') k = atoi(optarg), idx_par_set = 1;
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else if (c == 'H') is_hpc = 1, idx_par_set = 1;
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@ -96,6 +96,7 @@ int main(int argc, char *argv[])
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else if (c == 's') opt.min_dp_max = atoi(optarg);
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else if (c == 'I') batch_size = mm_parse_num(optarg);
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else if (c == 'K') minibatch_size = (int)mm_parse_num(optarg);
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else if (c == 'R') mm_set_rg(optarg); // WARNING: this modifies global variables in format.c
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else if (c == 0 && long_idx == 0) bucket_bits = atoi(optarg); // --bucket-bits
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else if (c == 0 && long_idx == 2) keep_name = 0; // --int-rname
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else if (c == 0 && long_idx == 3) mm_dbg_flag |= MM_DBG_NO_KALLOC; // --no-kalloc
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@ -194,14 +195,15 @@ int main(int argc, char *argv[])
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fprintf(stderr, " -s INT minimal peak DP alignment score [%d]\n", opt.min_dp_max);
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fprintf(stderr, " -u CHAR how to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG [n]\n");
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fprintf(stderr, " Input/Output:\n");
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fprintf(stderr, " -Q ignore base quality in the input\n");
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fprintf(stderr, " -a output in the SAM format (PAF by default)\n");
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fprintf(stderr, " -Q don't output base quality in SAM\n");
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fprintf(stderr, " -R STR SAM read group line in a format like '@RG\\tID:foo\\tSM:bar' []\n");
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fprintf(stderr, " -c output CIGAR in PAF\n");
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fprintf(stderr, " -S output the cs tag in PAF\n");
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fprintf(stderr, " -S output the cs tag in PAF (cs encodes both query and ref sequences)\n");
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fprintf(stderr, " -t INT number of threads [%d]\n", n_threads);
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fprintf(stderr, " -K NUM minibatch size [200M]\n");
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// fprintf(stderr, " -v INT verbose level [%d]\n", mm_verbose);
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fprintf(stderr, " -V show version number\n");
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fprintf(stderr, " --version show version number\n");
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fprintf(stderr, " Preset:\n");
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fprintf(stderr, " -x STR preset (recommended to be applied before other options) []\n");
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fprintf(stderr, " map10k/map-pb: -Hk19 (PacBio/ONT vs reference mapping)\n");
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6
map.c
6
map.c
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@ -386,11 +386,7 @@ int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int
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if (pl.fp == 0) return -1;
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pl.opt = opt, pl.mi = idx;
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pl.n_threads = n_threads, pl.mini_batch_size = mini_batch_size;
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if (opt->flag & MM_F_OUT_SAM) {
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uint32_t i;
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for (i = 0; i < idx->n_seq; ++i)
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printf("@SQ\tSN:%s\tLN:%d\n", idx->seq[i].name, idx->seq[i].len);
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}
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if (opt->flag & MM_F_OUT_SAM) sam_write_sam_header(idx);
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kt_pipeline(n_threads == 1? 1 : 2, worker_pipeline, &pl, 3);
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free(pl.str.s);
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mm_bseq_close(pl.fp);
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11
minimap2.1
11
minimap2.1
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@ -219,13 +219,18 @@ no attempt to match GT-AG [n]
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Cost of non-canonical splicing sites [0].
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.SS Input/output options
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.TP 10
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.B -Q
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Ignore base quality in the input file.
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.TP
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.B -a
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Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF
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by default.
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.TP
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.B -Q
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Ignore base quality in the input file.
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.TP
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.BI -R \ STR
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SAM read group line in a format like
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.B @RG\\\\tID:foo\\\\tSM:bar
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[].
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.TP
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.B -c
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Generate CIGAR. In PAF, the CIGAR is written to the `cg' custom tag.
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.TP
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2
mmpriv.h
2
mmpriv.h
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@ -40,6 +40,8 @@ void radix_sort_128x(mm128_t *beg, mm128_t *end);
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void radix_sort_64(uint64_t *beg, uint64_t *end);
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uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);
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void mm_set_rg(const char *s);
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void sam_write_sam_header(const mm_idx_t *idx);
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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);
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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);
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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);
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