41 lines
865 B
C
41 lines
865 B
C
#ifndef CMINIMAP2_H
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#define CMINIMAP2_H
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#include <stdlib.h>
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#include "minimap.h"
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typedef struct {
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const char *ctg;
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int32_t ctg_start, ctg_end;
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int32_t qry_start, qry_end;
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int32_t n_cigar32;
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uint8_t strand, mapq, is_primary;
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uint32_t *cigar32;
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} mm_hitpy_t;
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static inline mm_hitpy_t *mm_reg2hitpy(const mm_idx_t *mi, int n_regs, mm_reg1_t *regs)
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{
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mm_hitpy_t *h;
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int i;
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h = (mm_hitpy_t*)calloc(n_regs, sizeof(mm_hitpy_t));
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for (i = 0; i < n_regs; ++i) {
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mm_reg1_t *r = ®s[i];
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h[i].ctg = mi->seq[r->rid].name;
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h[i].ctg_start = r->rs, h[i].ctg_end = r->re;
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h[i].qry_start = r->qs, h[i].qry_end = r->qe;
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h[i].strand = r->rev;
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h[i].mapq = r->mapq;
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h[i].is_primary = (r->id == r->parent);
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h[i].n_cigar32 = r->p->n_cigar;
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h[i].cigar32 = r->p->cigar;
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}
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return h;
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}
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static inline void mm_free_reg1(mm_reg1_t *r)
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{
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free(r->p);
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}
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#endif
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