42 lines
1.3 KiB
C
42 lines
1.3 KiB
C
#include <assert.h>
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#include "minimap.h"
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#include "ksw2.h"
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void mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int n_regs, mm_reg1_t *regs, mm128_t *a)
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{
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extern unsigned char seq_nt4_table[256];
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int i, k, reg;
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uint8_t *qseq0[2];
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qseq0[0] = (uint8_t*)kmalloc(km, qlen);
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qseq0[1] = (uint8_t*)kmalloc(km, qlen);
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for (i = 0; i < qlen; ++i) {
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qseq0[0][i] = seq_nt4_table[(uint8_t)qstr[i]];
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qseq0[1][qlen - 1 - i] = qseq0[0][i] < 4? 3 - qseq0[0][i] : 4;
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}
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for (reg = 0; reg < n_regs; ++reg) {
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mm_reg1_t *r = ®s[reg];
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int32_t rid = a[r->as].x<<1>>33, rev = a[r->as].x>>63;
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uint8_t *tseq;
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tseq = (uint8_t*)kmalloc(km, r->re - r->rs);
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for (i = 0; i < r->cnt - 1; ++i) {
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uint8_t *qseq;
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int32_t rs, re, qs, qe, ret;
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rs = (int32_t)a[r->as + i].x + 1;
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re = (int32_t)a[r->as + i + 1].x + 1;
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qs = (int32_t)a[r->as + i].y + 1;
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qe = (int32_t)a[r->as + i + 1].y + 1;
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qseq = &qseq0[rev][qs];
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ret = mm_idx_getseq(mi, rid, rs, re, tseq);
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assert(ret > 0);
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fprintf(stderr, "===> %d,%d (%s:%d-%d) <===\n", reg, i, mi->seq[rid].name, rs, re);
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for (k = 0; k < re - rs; ++k) fputc("ACGTN"[tseq[k]], stderr); fputc('\n', stderr);
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for (k = 0; k < qe - qs; ++k) fputc("ACGTN"[qseq[k]], stderr); fputc('\n', stderr);
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}
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kfree(km, tseq);
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}
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kfree(km, qseq0[0]); kfree(km, qseq0[1]);
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}
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