/* The MIT License

   Copyright (C) 2011 by Attractive Chaos <attractor@live.co.uk>

   Copyright (C) 2013-2018, 2020-2021, 2023, 2025-2026 Genome Research Ltd.

   Permission is hereby granted, free of charge, to any person obtaining

   a copy of this software and associated documentation files (the

   "Software"), to deal in the Software without restriction, including

   without limitation the rights to use, copy, modify, merge, publish,

   distribute, sublicense, and/or sell copies of the Software, and to

   permit persons to whom the Software is furnished to do so, subject to

   the following conditions:

   The above copyright notice and this permission notice shall be

   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,

   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF

   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND

   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS

   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN

   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN

   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE

   SOFTWARE.

*/

#define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h

#include <config.h>

#include <stdarg.h>

#include <stdio.h>

#include <ctype.h>

#include <string.h>

#include <stdint.h>

#include <math.h>

#include "htslib/kstring.h"

#include "htslib/hts_alloc.h"

int kputd(double d, kstring_t *s) {

  int len = 0;

  char buf[21], *cp = buf+20, *ep;

  if (d == 0) {

    if (signbit(d)) {

      kputsn("-0",2,s);

      return 2;

    } else {

      kputsn("0",1,s);

      return 1;

    }

  }

  if (d < 0) {

    kputc('-',s);

    len = 1;

    d=-d;

  }

  if (!(d >= 0.0001 && d <= 999999)) {

    if (ks_resize(s, s->l + 50) < 0)

      return EOF;

    // We let stdio handle the exponent cases

    int s2 = snprintf(s->s + s->l, s->m - s->l, "%g", d);

    len += s2;

    s->l += s2;

    return len;

  }

  // Correction for rounding - rather ugly

  // Optimised for small numbers.

  uint32_t i;

  if (d<0.001)         i = rint(d*1000000000), cp -= 1;

  else if (d < 0.01)   i = rint(d*100000000),  cp -= 2;

  else if (d < 0.1)    i = rint(d*10000000),   cp -= 3;

  else if (d < 1)      i = rint(d*1000000),    cp -= 4;

  else if (d < 10)     i = rint(d*100000),     cp -= 5;

  else if (d < 100)    i = rint(d*10000),      cp -= 6;

  else if (d < 1000)   i = rint(d*1000),       cp -= 7;

  else if (d < 10000)  i = rint(d*100),        cp -= 8;

  else if (d < 100000) i = rint(d*10),         cp -= 9;

  else                 i = rint(d),            cp -= 10;

  // integer i is always 6 digits, so print it 2 at a time.

  static const char kputuw_dig2r[] =

    "00010203040506070809"

    "10111213141516171819"

    "20212223242526272829"

    "30313233343536373839"

    "40414243444546474849"

    "50515253545556575859"

    "60616263646566676869"

    "70717273747576777879"

    "80818283848586878889"

    "90919293949596979899";

  memcpy(cp-=2, &kputuw_dig2r[2*(i%100)], 2); i /= 100;

  memcpy(cp-=2, &kputuw_dig2r[2*(i%100)], 2); i /= 100;

  memcpy(cp-=2, &kputuw_dig2r[2*(i%100)], 2);

  // Except when it rounds up (d=0.009999999 is i=1000000)

  if (i >= 100)

    *--cp = '0' + (i/100);

  int p = buf+20-cp;

  if (p <= 10) { /* d < 1 */

    // 0.00123 is 123, so add leading zeros and 0.

    ep = cp+5; // 6 precision

    while (p < 10) { // aka d < 1

      *--cp = '0';

      p++;

    }

    *--cp = '.';

    *--cp = '0';

  } else {

    // 123.001 is 123001 with p==13, so move 123 down and add "."

    // Equiv to memmove(cp-1, cp, p-10); cp--;

    char *xp = --cp;

    ep = cp+6;

    while (p > 10) {

      xp[0] = xp[1];

      xp++;

      p--;

    }

    xp[0] = '.';

  }

  // Cull trailing zeros

  while (*ep == '0' && ep > cp)

    ep--;

  // End can be 1 out due to the mostly-6 but occasionally 7 (i==1) case.

  // Also code with "123." which should be "123"

  if (*ep && *ep != '.')

    ep++;

  *ep = 0;

  int sl = ep-cp;

  len += sl;

  kputsn(cp, sl, s);

  return len;

}

int kvsprintf(kstring_t *s, const char *fmt, va_list ap)

{

  va_list args;

  int l;

  va_copy(args, ap);

  if (fmt[0] == '%' && fmt[1] == 'g' && fmt[2] == 0) {

    double d = va_arg(args, double);

    l = kputd(d, s);

    va_end(args);

    return l;

  }

  if (!s->s) {

    const size_t sz = 64;

    s->s = malloc(sz);

    if (!s->s)

      return -1;

    s->m = sz;

    s->l = 0;

  }

  l = vsnprintf(s->s + s->l, s->m - s->l, fmt, args); // This line does not work with glibc 2.0. See `man snprintf'.

  va_end(args);

  if (l + 1 > s->m - s->l) {

    if (ks_resize(s, s->l + l + 2) < 0)

      return -1;

    va_copy(args, ap);

    l = vsnprintf(s->s + s->l, s->m - s->l, fmt, args);

    va_end(args);

  }

  s->l += l;

  return l;

}

int ksprintf(kstring_t *s, const char *fmt, ...)

{

  va_list ap;

  int l;

  va_start(ap, fmt);

  l = kvsprintf(s, fmt, ap);

  va_end(ap);

  return l;

}

char *kstrtok(const char *str, const char *sep_in, ks_tokaux_t *aux)

{

  const unsigned char *p, *start, *sep = (unsigned char *) sep_in;

  if (sep) { // set up the table

    if (str == 0 && aux->finished) return 0; // no need to set up if we have finished

    aux->finished = 0;

    if (sep[0] && sep[1]) {

      aux->sep = -1;

      aux->tab[0] = aux->tab[1] = aux->tab[2] = aux->tab[3] = 0;

      for (p = sep; *p; ++p) aux->tab[*p>>6] |= 1ull<<(*p&0x3f);

    } else aux->sep = sep[0];

  }

  if (aux->finished) return 0;

  else if (str) start = (unsigned char *) str, aux->finished = 0;

  else start = (unsigned char *) aux->p + 1;

  if (aux->sep < 0) {

    for (p = start; *p; ++p)

      if (aux->tab[*p>>6]>>(*p&0x3f)&1) break;

  } else {

    // Using strchr is fast for next token, but slower for

    // last token due to extra pass from strlen.  Overall

    // on a VCF parse this func was 146% faster with // strchr.

    // Equiv to:

    // for (p = start; *p; ++p) if (*p == aux->sep) break;

    // NB: We could use strchrnul() here from glibc if detected,

    // which is ~40% faster again, but it's not so portable.

    // i.e.   p = (uint8_t *)strchrnul((char *)start, aux->sep);

    uint8_t *p2 = (uint8_t *)strchr((char *)start, aux->sep);

    p = p2 ? p2 : start + strlen((char *)start);

  }

  aux->p = (const char *) p; // end of token

  if (*p == 0) aux->finished = 1; // no more tokens

  return (char*)start;

}

// s MUST BE a null terminated string; l = strlen(s)

int ksplit_core(char *s, int delimiter, int *_max, int **_offsets)

{

  int i, n, max, last_char, last_start, *offsets, l;

  n = 0; max = *_max; offsets = *_offsets;

  l = strlen(s);

#define __ksplit_aux do {           \

    if (_offsets) {           \

      s[i] = 0;         \

      if (n == max) {         \

        int *tmp;       \

        max = max? max<<1 : 2;     \

        if ((tmp = hts_realloc_p(offsets, sizeof(int), max))) {  \

          offsets = tmp;      \

        } else {       \

          free(offsets);      \

          *_offsets = NULL;   \

          return 0;     \

        }          \

      }           \

      offsets[n++] = last_start;      \

    } else ++n;           \

  } while (0)

  for (i = 0, last_char = last_start = 0; i <= l; ++i) {

    if (delimiter == 0) {

      if (isspace((int)((unsigned char) s[i])) || s[i] == 0) {

        if (isgraph(last_char))

                    __ksplit_aux; // the end of a field

      } else {

        if (isspace(last_char) || last_char == 0)

                    last_start = i;

      }

    } else {

      if (s[i] == delimiter || s[i] == 0) {

        if (last_char != 0 && last_char != delimiter) __ksplit_aux; // the end of a field

      } else {

        if (last_char == delimiter || last_char == 0) last_start = i;

      }

    }

    last_char = (int)((unsigned char)s[i]);

  }

  *_max = max; *_offsets = offsets;

  return n;

}

int kgetline(kstring_t *s, kgets_func *fgets_fn, void *fp)

{

  size_t l0 = s->l;

  while (s->l == l0 || s->s[s->l-1] != '\n') {

    if (s->m - s->l < 200) {

      if (ks_resize(s, s->m + 200) < 0)

        return EOF;

    }

    if (fgets_fn(s->s + s->l, s->m - s->l, fp) == NULL) break;

    s->l += strlen(s->s + s->l);

  }

  if (s->l == l0) return EOF;

  if (s->l > l0 && s->s[s->l-1] == '\n') {

    s->l--;

    if (s->l > l0 && s->s[s->l-1] == '\r') s->l--;

  }

  s->s[s->l] = '\0';

  return 0;

}

// Wrap around fgets to get the right signature for kgets_func

static char * fgets_wrapper(char *buffer, int size, void *stream)

{

    return fgets(buffer, size, (FILE *) stream);

}

int kfgetline(kstring_t *s, FILE *fp)

{

    if (!s || !fp)

        return EOF;

    return kgetline(s, fgets_wrapper, fp);

}

int kgetline2(kstring_t *s, kgets_func2 *fgets_fn, void *fp)

{

  size_t l0 = s->l;

  while (s->l == l0 || s->s[s->l-1] != '\n') {

    if (s->m - s->l < 200) {

      // We return EOF for both EOF and error and the caller

      // needs to check for errors in fp, and we haven't

      // even got there yet.

      //

      // The only way of propagating memory errors is to

      // deliberately call something that we know triggers

      // and error so fp is also set.  This works for

      // hgets, but not for gets where reading <= 0 bytes

      // isn't an error.

      if (ks_resize(s, s->m + 200) < 0) {

        fgets_fn(s->s + s->l, 0, fp);

        return EOF;

      }

    }

    ssize_t len = fgets_fn(s->s + s->l, s->m - s->l, fp);

    if (len <= 0) break;

    s->l += len;

  }

  if (s->l == l0) return EOF;

  if (s->l > l0 && s->s[s->l-1] == '\n') {

    s->l--;

    if (s->l > l0 && s->s[s->l-1] == '\r') s->l--;

  }

  s->s[s->l] = '\0';

  return 0;

}

typedef unsigned char ubyte_t;

/**********************

 * Karp-Rabin search  *

 **********************/

// Backup solution for when we can't use Boyer-Moore, e.g. due to memory

// required.  Karp-Rabin only needs to store a couple of hash values

// so will always complete.

static uint64_t fast_exp(uint64_t x, uint64_t n)

{

  uint64_t y = 1;

  if (n == 0)

    return 1;

  while (n > 1) {

    if (n & 1)

      y *= x;

    x *= x;

    n >>= 1;

  }

  return y * x;

}

static void * karp_rabin(const void *str_, size_t n, const void *pat_, size_t m)

{

  const ubyte_t *str = (const ubyte_t *) str_;

  const ubyte_t *pat = (const ubyte_t *) pat_;

  const uint64_t b = 31;

  uint64_t hash_pat = 0;

  uint64_t hash_str = 0;

  uint64_t b_to_m = fast_exp(b, m);

  size_t i;

  ubyte_t mismatch = 0;

  if (m > n)

    return NULL;

  // Calculate hash of pat and initial part of str.

  for (i = 0; i < m; i++) {

    mismatch |= str[i] ^ pat[i];

    hash_pat = hash_pat * b + pat[i] + 1U;

    hash_str = hash_str * b + str[i] + 1U;

  }

  if (!mismatch) // Match found at start (or m == 0)

    return (void *) str_;

  for (; i < n; i++) {

    hash_str = hash_str * b + str[i] + 1U - b_to_m * (str[i - m] + 1U);

    if (hash_str == hash_pat) {

      if (memcmp(pat, str + i + 1 - m, m) == 0)

        return (void *) (str + i + 1 - m);

    }

  }

  return NULL;

}

/**********************

 * Boyer-Moore search *

 **********************/

// reference: http://www-igm.univ-mlv.fr/~lecroq/string/node14.html

static int *ksBM_prep(const ubyte_t *pat, int m)

{

  int i, *suff, *prep, *bmGs, *bmBc;

  if (m < 1)

    return NULL;

  prep = hts_calloc_ps(sizeof(int), m, 256);

  if (!prep) return NULL;

  bmGs = prep; bmBc = prep + m;

  { // preBmBc()

    for (i = 0; i < 256; ++i) bmBc[i] = m;

    for (i = 0; i < m - 1; ++i) bmBc[pat[i]] = m - i - 1;

  }

  suff = (int*)calloc(m, sizeof(int));

  if (!suff) { free(prep); return NULL; }

  { // suffixes()

    int f = 0, g;

    suff[m - 1] = m;

    g = m - 1;

    for (i = m - 2; i >= 0; --i) {

      if (i > g && suff[i + m - 1 - f] < i - g)

        suff[i] = suff[i + m - 1 - f];

      else {

        if (i < g) g = i;

        f = i;

        while (g >= 0 && pat[g] == pat[g + m - 1 - f]) --g;

        suff[i] = f - g;

      }

    }

  }

  { // preBmGs()

    int j = 0;

    for (i = 0; i < m; ++i) bmGs[i] = m;

    for (i = m - 1; i >= 0; --i)

      if (suff[i] == i + 1)

        for (; j < m - 1 - i; ++j)

          if (bmGs[j] == m)

            bmGs[j] = m - 1 - i;

    for (i = 0; i <= m - 2; ++i)

      bmGs[m - 1 - suff[i]] = m - 1 - i;

  }

  free(suff);

  return prep;

}

static void *boyer_moore(const void *str_, size_t n, const void *pat_, int m,

             int **stored_prep_ptr)

{

  size_t j;

  int i, *prep = 0, *bmGs, *bmBc;

  const ubyte_t *str, *pat;

  if (!str_ || !pat_)

    return (void *) str_;

  str = (const ubyte_t*) str_;

  pat = (const ubyte_t*) pat_;

  if (m <= 0) // Empty string always matches at the start

    return (void *) str_;

  if (n < m)  // Input shorter than pattern can't match

    return NULL;

  if (m == 1) // Switch to memchr for 1 byte patterns (likely faster)

    return (void *)memchr(str, pat[0], n);

  if (stored_prep_ptr && *stored_prep_ptr) {

    prep = *stored_prep_ptr;

  } else {

    prep = ksBM_prep(pat, m);

    if (!prep) return karp_rabin(str_, n, pat_, m);

    if (stored_prep_ptr)

      *stored_prep_ptr = prep;

  }

  bmGs = prep;      // Good-suffix shift array

  bmBc = prep + m;  // Bad character shift array

  j = 0;

  while (j <= n - m) {

    for (i = m - 1; i >= 0 && pat[i] == str[i+j]; --i);

    if (i >= 0) {

      int max = bmBc[str[i+j]] - m + 1 + i;

      if (max < bmGs[i]) max = bmGs[i];

      j += max;

    } else { // Match found

      if (!stored_prep_ptr) free(prep);

      return (void*)(str + j);

    }

  }

  // No match

  if (!stored_prep_ptr) free(prep);

  return NULL;

}

void *kmemmem(const void *str, int n, const void *pat, int m, int **prep)

{

  return boyer_moore(str, n >= 0 ? n : 0, pat, m, prep);

}

char *kstrstr(const char *str, const char *pat, int **prep)

{

  size_t patlen = strlen(pat);

  if (patlen <= INT_MAX)

    return (char*)boyer_moore(str, strlen(str), pat, patlen, prep);

  else

    return karp_rabin(str, strlen(str), pat, patlen);

}

char *kstrnstr(const char *str, const char *pat, int n, int **prep)

{

  if (!pat || *pat == '\0')

    return (char *) str;

  if (n <= 0)

    return NULL;

  const char *endp = memchr(str, '\0', n);

  if (endp != NULL && endp - str < n)

    n = endp - str;

  size_t patlen = strlen(pat);

  if (patlen > n)

    return NULL;

  return (char*)boyer_moore(str, n, pat, patlen, prep);

}

/***********************

 * The main() function *

 ***********************/

#ifdef KSTRING_MAIN

#include <stdio.h>

int main()

{

  kstring_t *s;

  int *fields, n, i;

  ks_tokaux_t aux;

  char *p;

  s = (kstring_t*)calloc(1, sizeof(kstring_t));

  // test ksprintf()

  ksprintf(s, " abcdefg:    %d ", 100);

  printf("'%s'\n", s->s);

  // test ksplit()

  fields = ksplit(s, 0, &n);

  for (i = 0; i < n; ++i)

    printf("field[%d] = '%s'\n", i, s->s + fields[i]);

  // test kstrtok()

  s->l = 0;

  for (p = kstrtok("ab:cde:fg/hij::k", ":/", &aux); p; p = kstrtok(0, 0, &aux)) {

    kputsn(p, aux.p - p, s);

    kputc('\n', s);

  }

  printf("%s", s->s);

  // free

  free(s->s); free(s); free(fields);

  {

    static char *str = "abcdefgcdgcagtcakcdcd";

    static char *pat = "cd";

    char *ret, *s = str;

    int *prep = 0;

    while ((ret = kstrstr(s, pat, &prep)) != 0) {

      printf("match: %s\n", ret);

      s = ret + prep[0];

    }

    free(prep);

  }

  return 0;

}

#endif