34 lines
1.1 KiB
C
34 lines
1.1 KiB
C
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#ifndef COMMON_H_
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#define COMMON_H_
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#define OCC_INTV_SHIFT 5
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#define OCC_INTERVAL (1LL << OCC_INTV_SHIFT)
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#define OCC_INTV_MASK (OCC_INTERVAL - 1)
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#define bwt_B00(b, k) ((b)->bwt[(k) >> 4] >> ((~(k) & 0xf) << 1) & 3)
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/* retrieve a character from the $-removed BWT string. Note that
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* bwt_t::bwt is not exactly the BWT string and therefore this macro is
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* called bwt_B0 instead of bwt_B */
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#define bwt_B0(b, k) (bwt_bwt(b, k) >> ((~(k) & 0xf) << 1) & 3)
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#define bwt_set_intv(bwt, c, ik) ((ik).x[0] = (bwt)->L2[(int)(c)] + 1, (ik).x[2] = (bwt)->L2[(int)(c) + 1] - (bwt)->L2[(int)(c)], (ik).x[1] = (bwt)->L2[3 - (c)] + 1, (ik).info = 0)
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#define SA_BYTES_33(n_sa) ((((33 * (n_sa) + 7) / 8) & (~7L)) + 8)
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#define SA_BYTES_40(n_sa) ((((40 * (n_sa) + 7) / 8) & (~7L)) + 8)
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#define xassert(cond, msg) \
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if ((cond) == 0) \
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_err_fatal_simple_core(__func__, msg)
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typedef uint64_t bwtint_t;
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double realtime(void);
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void bwt_set_sa_33(uint8_t *sa_arr, bwtint_t k, bwtint_t val);
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bwtint_t bwt_get_sa_33(uint8_t *sa_arr, bwtint_t k);
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int main_sa(int argc, char **argv);
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int main_fmtidx(int argc, char **argv);
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#endif
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