40 lines
893 B
C
40 lines
893 B
C
#ifndef CMAPPY_H
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#define CMAPPY_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 blen, NM, ctg_len;
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uint8_t mapq, is_primary;
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int8_t strand, trans_strand;
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int32_t n_cigar32;
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uint32_t *cigar32;
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} mm_hitpy_t;
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static inline void mm_reg2hitpy(const mm_idx_t *mi, mm_reg1_t *r, mm_hitpy_t *h)
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{
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h->ctg = mi->seq[r->rid].name;
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h->ctg_len = mi->seq[r->rid].len;
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h->ctg_start = r->rs, h->ctg_end = r->re;
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h->qry_start = r->qs, h->qry_end = r->qe;
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h->strand = r->rev? -1 : 1;
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h->mapq = r->mapq;
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h->blen = r->p->blen;
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h->NM = r->p->n_diff;
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h->trans_strand = r->p->trans_strand == 1? 1 : r->p->trans_strand == 2? -1 : 0;
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h->is_primary = (r->id == r->parent);
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h->n_cigar32 = r->p->n_cigar;
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h->cigar32 = r->p->cigar;
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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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