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multi-seg working on toy examples

This commit is contained in:
Heng Li 2017-09-25 13:42:04 -04:00
parent a742f10164
commit 3bb66e1ed3
6 changed files with 62 additions and 16 deletions
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19
bseq.c
View File

@ -7,6 +7,25 @@
#include "kseq.h"
KSEQ_INIT2(, gzFile, gzread)
unsigned char seq_comp_table[256] = {
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63,
64, 'T', 'V', 'G', 'H', 'E', 'F', 'C', 'D', 'I', 'J', 'M', 'L', 'K', 'N', 'O',
'P', 'Q', 'Y', 'S', 'A', 'A', 'B', 'W', 'X', 'R', 'Z', 91, 92, 93, 94, 95,
64, 't', 'v', 'g', 'h', 'e', 'f', 'c', 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o',
'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', 123, 124, 125, 126, 127,
128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143,
144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159,
160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175,
176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191,
192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207,
208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223,
224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239,
240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255
};
#define CHECK_PAIR_THRES 1000000
struct mm_bseq_file_s {

19
bseq.h
View File

@ -24,6 +24,7 @@ mm_bseq1_t *mm_bseq_read_multi(int n_fp, mm_bseq_file_t **fp, int chunk_size, in
int mm_bseq_eof(mm_bseq_file_t *fp);
extern unsigned char seq_nt4_table[256];
extern unsigned char seq_comp_table[256];
static inline int mm_qname_same(const char *s1, const char *s2)
{
@ -31,11 +32,25 @@ static inline int mm_qname_same(const char *s1, const char *s2)
l1 = strlen(s1);
l2 = strlen(s2);
if (l1 != l2 || l1 < 3) return 0;
if (!(s1[l1-1] >= '1' && s1[l1-1] <= '2' && s1[l1-2] == '/')) return 0;
if (!(s2[l2-1] >= '1' && s2[l2-1] <= '2' && s2[l2-2] == '/')) return 0;
if (!(s1[l1-1] >= '0' && s1[l1-1] <= '9' && s1[l1-2] == '/')) return 0;
if (!(s2[l2-1] >= '0' && s2[l2-1] <= '9' && s2[l2-2] == '/')) return 0;
return (strncmp(s1, s2, l1 - 2) == 0);
}
static inline void mm_revcomp_bseq(mm_bseq1_t *s)
{
int i, t, l = s->l_seq;
for (i = 0; i < l>>1; ++i) {
t = s->seq[l - i - 1];
s->seq[l - i - 1] = seq_comp_table[(uint8_t)s->seq[i]];
s->seq[i] = seq_comp_table[t];
}
if (l&1) s->seq[l>>1] = seq_comp_table[(uint8_t)s->seq[l>>1]];
if (s->qual)
for (i = 0; i < l>>1; ++i)
t = s->qual[l - i - 1], s->qual[l - i - 1] = s->qual[i], s->qual[i] = t;
}
#ifdef __cplusplus
}
#endif

14
format.c
View File

@ -213,17 +213,6 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
write_cs(km, s, mi, t, r);
}
static char comp_tab[] = {
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63,
64, 'T', 'V', 'G', 'H', 'E', 'F', 'C', 'D', 'I', 'J', 'M', 'L', 'K', 'N', 'O',
'P', 'Q', 'Y', 'S', 'A', 'A', 'B', 'W', 'X', 'R', 'Z', 91, 92, 93, 94, 95,
64, 't', 'v', 'g', 'h', 'e', 'f', 'c', 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o',
'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', 123, 124, 125, 126, 127
};
void mm_write_sam_SQ(const mm_idx_t *idx)
{
uint32_t i;
@ -233,12 +222,13 @@ void mm_write_sam_SQ(const mm_idx_t *idx)
static void sam_write_sq(kstring_t *s, char *seq, int l, int rev, int comp)
{
extern unsigned char seq_comp_table[256];
if (rev) {
int i;
str_enlarge(s, l);
for (i = 0; i < l; ++i) {
int c = seq[l - 1 - i];
s->s[s->l + i] = c < 128 && comp? comp_tab[c] : c;
s->s[s->l + i] = c < 128 && comp? seq_comp_table[c] : c;
}
s->l += l;
} else str_copy(s, seq, seq + l);

6
main.c
View File

@ -37,6 +37,9 @@ static struct option long_options[] = {
{ "cost-non-gt-ag", required_argument, 0, 0 },
{ "no-sam-sq", no_argument, 0, 0 },
{ "sr", no_argument, 0, 0 },
{ "multi-segment", no_argument, 0, 0 },
{ "2nd-seg-rev", no_argument, 0, 0 },
{ "2nd-seg-for", no_argument, 0, 0 },
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@ -115,6 +118,9 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx ==11) opt.noncan = atoi(optarg); // --cost-non-gt-ag
else if (c == 0 && long_idx ==12) opt.flag |= MM_F_NO_SAM_SQ; // --no-sam-sq
else if (c == 0 && long_idx ==13) opt.flag |= MM_F_SR; // --sr
else if (c == 0 && long_idx ==14) opt.flag |= MM_F_MULTI_SEG; // --multi-seg
else if (c == 0 && long_idx ==15) opt.flag |= MM_F_SEG_REV; // --2nd-seg-rev
else if (c == 0 && long_idx ==16) opt.flag &= ~MM_F_SEG_REV; // --2nd-seg-for
else if (c == 'V') {
puts(MM_VERSION);
return 0;

19
map.c
View File

@ -75,7 +75,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
mo->min_dp_max = 200;
} else if (strcmp(preset, "short") == 0 || strcmp(preset, "sr") == 0) {
io->is_hpc = 0, io->k = 21, io->w = 11;
mo->flag |= MM_F_SR | MM_F_MULTI_SEG;
mo->flag |= MM_F_SR | MM_F_MULTI_SEG | MM_F_SEG_REV;
mo->a = 2, mo->b = 8, mo->q = 12, mo->e = 2, mo->q2 = 32, mo->e2 = 1;
mo->max_gap = 100;
mo->pri_ratio = 0.5f;
@ -161,7 +161,7 @@ static void collect_minimizers(const mm_mapopt_t *opt, const mm_idx_t *mi, int n
for (i = n = 0; i < n_segs; ++i) {
mm_sketch(b->km, seqs[i], qlens[i], mi->w, mi->k, i, mi->is_hpc, &b->mini);
for (j = n; j < b->mini.n; ++j)
b->mini.a[j].x += sum << 1;
b->mini.a[j].y += sum << 1;
if (opt->sdust_thres > 0) // mask low-complexity minimizers
b->mini.n = n + mm_dust_minier(b->mini.n - n, b->mini.a + n, qlens[i], seqs[i], opt->sdust_thres, b->sdb);
sum += qlens[i], n = b->mini.n;
@ -295,6 +295,7 @@ void mm_map_multi(const mm_idx_t *mi, int n_segs, const int *qlens, const char *
seg = mm_seg_gen(b->km, n_segs, qlens, n_regs0, regs0, n_regs, regs, a);
free(regs0);
for (i = 0; i < n_segs; ++i) {
mm_set_parent(b->km, opt->mask_level, n_regs[i], regs[i], opt->a * 2 + opt->b);
regs[i] = align_regs(opt, mi, b->km, qlens[i], seqs[i], &n_regs[i], regs[i], seg[i].a);
mm_set_mapq(n_regs[i], regs[i], opt->min_chain_score, opt->a, rep_len);
}
@ -344,10 +345,24 @@ static void worker_for(void *_data, long i, int tid) // kt_for() callback
qlens = (int*)kmalloc(b->km, s->n_seg[i] * sizeof(int));
qseqs = (const char**)kmalloc(b->km, s->n_seg[i] * sizeof(const char**));
for (j = 0; j < s->n_seg[i]; ++j) {
if (j > 0 && (s->p->opt->flag & MM_F_SEG_REV))
mm_revcomp_bseq(&s->seq[off + j]);
qlens[j] = s->seq[off + j].l_seq;
qseqs[j] = s->seq[off + j].seq;
}
mm_map_multi(s->p->mi, s->n_seg[i], qlens, qseqs, &s->n_reg[off], &s->reg[off], b, s->p->opt, s->seq[off].name);
if (s->n_seg[i] > 1 && (s->p->opt->flag & MM_F_SEG_REV))
for (j = 1; j < s->n_seg[i]; ++j) { // flip the query strand and coordinate to the original read strand
int k, t;
mm_revcomp_bseq(&s->seq[off + j]);
for (k = 0; k < s->n_reg[off + j]; ++k) {
mm_reg1_t *r = &s->reg[off + j][k];
t = r->qs;
r->qs = qlens[j] - r->qe;
r->qe = qlens[j] - t;
r->rev = !r->rev;
}
}
kfree(b->km, qlens);
kfree(b->km, qseqs);
}

1
minimap.h
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@ -18,6 +18,7 @@
#define MM_F_NO_SAM_SQ 0x800
#define MM_F_SR 0x1000
#define MM_F_MULTI_SEG 0x2000
#define MM_F_SEG_REV 0x4000
#define MM_IDX_MAGIC "MMI\2"