fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-09-15 21:17:54 +08:00
Code Issues Packages Projects Releases Wiki Activity

r670: added PE support to mappy

Browse Source 
and minor code cleanup
This commit is contained in:
Heng Li
2018-01-31 11:33:08 -05:00
parent 12a5a5fa3c
commit 46d6349af4
9 changed files with 71 additions and 23 deletions
Download Patch File Download Diff File Expand all files Collapse all files

33
python/cmappy.h
View File

@@ -15,6 +15,7 @@ typedef struct {
int32_t blen, mlen, NM, ctg_len;
uint8_t mapq, is_primary;
int8_t strand, trans_strand;
int32_t seg_id;
int32_t n_cigar32;
uint32_t *cigar32;
} mm_hitpy_t;
@@ -32,6 +33,7 @@ static inline void mm_reg2hitpy(const mm_idx_t *mi, mm_reg1_t *r, mm_hitpy_t *h)
h->NM = r->blen - r->mlen + r->p->n_ambi;
h->trans_strand = r->p->trans_strand == 1? 1 : r->p->trans_strand == 2? -1 : 0;
h->is_primary = (r->id == r->parent);
h->seg_id = r->seg_id;
h->n_cigar32 = r->p->n_cigar;
h->cigar32 = r->p->cigar;
}
@@ -68,4 +70,35 @@ static inline void mm_reset_timer(void)
mm_realtime0 = realtime();
}
extern unsigned char seq_comp_table[256];
static inline mm_reg1_t *mm_map_aux(const mm_idx_t *mi, const char *seq1, const char *seq2, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt)
{
if (seq2 == 0) {
return mm_map(mi, strlen(seq1), seq1, n_regs, b, opt, NULL);
} else {
int _n_regs[2];
mm_reg1_t *regs[2];
char *seq[2];
int i, len[2];
len[0] = strlen(seq1);
len[1] = strlen(seq2);
seq[0] = (char*)seq1;
seq[1] = strdup(seq2);
for (i = 0; i < len[1]>>1; ++i) {
int t = seq[1][len[1] - i - 1];
seq[1][len[1] - i - 1] = seq_comp_table[(uint8_t)seq[1][i]];
seq[1][i] = seq_comp_table[t];
}
if (len[1]&1) seq[1][len[1]>>1] = seq_comp_table[(uint8_t)seq[1][len[1]>>1]];
mm_map_frag(mi, 2, len, (const char**)seq, _n_regs, regs, b, opt, NULL);
for (i = 0; i < _n_regs[1]; ++i)
regs[1][i].rev = !regs[1][i].rev;
*n_regs = _n_regs[0] + _n_regs[1];
regs[0] = (mm_reg1_t*)realloc(regs[0], sizeof(mm_reg1_t) * (*n_regs));
memcpy(&regs[0][_n_regs[0]], regs[1], _n_regs[1] * sizeof(mm_reg1_t));
free(regs[1]);
return regs[0];
}
}
#endif