text: /* The MIT License
  
     Copyright (C) 2011 by Attractive Chaos <attractor@live.co.uk>
     Copyright (C) 2013-2014, 2016, 2018-2019 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.
  */
  
  #ifndef KSTRING_H
  #define KSTRING_H
  
  #include <stdlib.h>
  #include <string.h>
  #include <stdarg.h>
  #include <stdint.h>
  #include <stdio.h>
  #include <limits.h>
  #include <sys/types.h>
  
  #ifndef kroundup32
  #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
  #endif
  
  #ifndef kroundup_size_t
  #define kroundup_size_t(x) (--(x),                                       \
                              (x)|=(x)>>(sizeof(size_t)/8), /*  0 or  1 */ \
                              (x)|=(x)>>(sizeof(size_t)/4), /*  1 or  2 */ \
                              (x)|=(x)>>(sizeof(size_t)/2), /*  2 or  4 */ \
                              (x)|=(x)>>(sizeof(size_t)),   /*  4 or  8 */ \
                              (x)|=(x)>>(sizeof(size_t)*2), /*  8 or 16 */ \
                              (x)|=(x)>>(sizeof(size_t)*4), /* 16 or 32 */ \
                              ++(x))
  #endif
  
  #ifndef HTS_COMPILER_HAS
  #define HTS_COMPILER_HAS(attribute) 0
  #endif
  #ifndef HTS_GCC_AT_LEAST
  #define HTS_GCC_AT_LEAST(major, minor) 0
  #endif
  
  #if defined(_WIN32) || defined(__CYGWIN__)
  #define HTS_DLL_EXPORT __declspec(dllexport)
  #elif HTS_COMPILER_HAS(__visibility__) || HTS_GCC_AT_LEAST(4,0)
  #define HTS_DLL_EXPORT __attribute__((__visibility__("default")))
  #elif defined(__SUNPRO_C) && __SUNPRO_C >= 0x550
  #define HTS_DLL_EXPORT __global
  #else
  #define HTS_DLL_EXPORT
  #endif
  
  #if !(defined(_WIN32) || defined(__CYGWIN__)) || defined(HTS_BUILDING_LIBRARY)
  #define HTSLIB_EXPORT HTS_DLL_EXPORT
  #else
  #define HTSLIB_EXPORT
  #endif
  
  #if defined __GNUC__ && (__GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ > 4))
  #ifdef __MINGW_PRINTF_FORMAT
  #define KS_ATTR_PRINTF(fmt, arg) __attribute__((__format__ (__MINGW_PRINTF_FORMAT, fmt, arg)))
  #else
  #define KS_ATTR_PRINTF(fmt, arg) __attribute__((__format__ (__printf__, fmt, arg)))
  #endif // __MINGW_PRINTF_FORMAT
  #else
  #define KS_ATTR_PRINTF(fmt, arg)
  #endif
  
  #ifndef HAVE___BUILTIN_CLZ
  #if defined __GNUC__ && (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
  #define HAVE___BUILTIN_CLZ 1
  #endif
  #endif
  
  /* kstring_t is a simple non-opaque type whose fields are likely to be
   * used directly by user code (but see also ks_str() and ks_len() below).
   * A kstring_t object is initialised by either of
   *       kstring_t str = KS_INITIALIZE;
   *       kstring_t str; ...; ks_initialize(&str);
   * and either ownership of the underlying buffer should be given away before
   * the object disappears (see ks_release() below) or the kstring_t should be
   * destroyed with  ks_free(&str) or free(str.s) */
  #ifndef KSTRING_T
  #define KSTRING_T kstring_t
  typedef struct kstring_t {
  	size_t l, m;
  	char *s;
  } kstring_t;
  #endif
  
  typedef struct {
  	uint64_t tab[4];
  	int sep, finished;
  	const char *p; // end of the current token
  } ks_tokaux_t;
  
  #ifdef __cplusplus
  extern "C" {
  #endif
  
      HTSLIB_EXPORT
  	int kvsprintf(kstring_t *s, const char *fmt, va_list ap) KS_ATTR_PRINTF(2,0);
  
      HTSLIB_EXPORT
  	int ksprintf(kstring_t *s, const char *fmt, ...) KS_ATTR_PRINTF(2,3);
  
      HTSLIB_EXPORT
      int kputd(double d, kstring_t *s); // custom %g only handler
  
      HTSLIB_EXPORT
  	int ksplit_core(char *s, int delimiter, int *_max, int **_offsets);
  
      HTSLIB_EXPORT
  	char *kstrstr(const char *str, const char *pat, int **_prep);
  
      HTSLIB_EXPORT
  	char *kstrnstr(const char *str, const char *pat, int n, int **_prep);
  
      HTSLIB_EXPORT
  	void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep);
  
  	/* kstrtok() is similar to strtok_r() except that str is not
  	 * modified and both str and sep can be NULL. For efficiency, it is
  	 * actually recommended to set both to NULL in the subsequent calls
  	 * if sep is not changed. */
      HTSLIB_EXPORT
  	char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux);
  
  	/* kgetline() uses the supplied fgets()-like function to read a "\n"-
  	 * or "\r\n"-terminated line from fp.  The line read is appended to the
  	 * kstring without its terminator and 0 is returned; EOF is returned at
  	 * EOF or on error (determined by querying fp, as per fgets()). */
  	typedef char *kgets_func(char *, int, void *);
      HTSLIB_EXPORT
  	int kgetline(kstring_t *s, kgets_func *fgets, void *fp);
  
      // This matches the signature of hgetln(), apart from the last pointer
  	typedef ssize_t kgets_func2(char *, size_t, void *);
      HTSLIB_EXPORT
  	int kgetline2(kstring_t *s, kgets_func2 *fgets, void *fp);
  
  #ifdef __cplusplus
  }
  #endif
  
  /// kstring initializer for structure assignment
  #define KS_INITIALIZE { 0, 0, NULL }
  
  /// kstring initializer for pointers
  /**
     @note Not to be used if the buffer has been allocated.  Use ks_release()
     or ks_clear() instead.
  */
  
  static inline void ks_initialize(kstring_t *s)
  {
      s->l = s->m = 0;
      s->s = NULL;
  }
  
  /// Resize a kstring to a given capacity
  static inline int ks_resize(kstring_t *s, size_t size)
  {
  	if (s->m < size) {
  		char *tmp;
  		kroundup_size_t(size);
  		tmp = (char*)realloc(s->s, size);
  		if (!tmp && size)
  		    return -1;
  		s->s = tmp;
  		s->m = size;
  	}
  	return 0;
  }
  
  /// Increase kstring capacity by a given number of bytes
  static inline int ks_expand(kstring_t *s, size_t expansion)
  {
      size_t new_size = s->l + expansion;
  
      if (new_size < s->l) // Overflow check
          return -1;
      return ks_resize(s, new_size);
  }
  
  /// Returns the kstring buffer
  static inline char *ks_str(kstring_t *s)
  {
  	return s->s;
  }
  
  /// Returns the kstring buffer, or an empty string if l == 0
  /**
   * Unlike ks_str(), this function will never return NULL.  If the kstring is
   * empty it will return a read-only empty string.  As the returned value
   * may be read-only, the caller should not attempt to modify it.
   */
  static inline const char *ks_c_str(kstring_t *s)
  {
      return s->l && s->s ? s->s : "";
  }
  
  static inline size_t ks_len(kstring_t *s)
  {
  	return s->l;
  }
  
  /// Reset kstring length to zero
  /**
     @return The kstring itself
  
     Example use: kputsn(string, len, ks_clear(s))
  */
  static inline kstring_t *ks_clear(kstring_t *s)
  {
      s->l = 0;
      return s;
  }
  
  // Give ownership of the underlying buffer away to something else (making
  // that something else responsible for freeing it), leaving the kstring_t
  // empty and ready to be used again, or ready to go out of scope without
  // needing  free(str.s)  to prevent a memory leak.
  static inline char *ks_release(kstring_t *s)
  {
  	char *ss = s->s;
  	s->l = s->m = 0;
  	s->s = NULL;
  	return ss;
  }
  
  /// Safely free the underlying buffer in a kstring.
  static inline void ks_free(kstring_t *s)
  {
      if (s) {
          free(s->s);
          ks_initialize(s);
      }
  }
  
  static inline int kputsn(const char *p, size_t l, kstring_t *s)
  {
  	size_t new_sz = s->l + l + 2;
  	if (new_sz <= s->l || ks_resize(s, new_sz) < 0)
  		return EOF;
  	memcpy(s->s + s->l, p, l);
  	s->l += l;
  	s->s[s->l] = 0;
  	return l;
  }
  
  static inline int kputs(const char *p, kstring_t *s)
  {
  	return kputsn(p, strlen(p), s);
  }
  
  static inline int kputc(int c, kstring_t *s)
  {
  	if (ks_resize(s, s->l + 2) < 0)
  		return EOF;
  	s->s[s->l++] = c;
  	s->s[s->l] = 0;
  	return (unsigned char)c;
  }
  
  static inline int kputc_(int c, kstring_t *s)
  {
  	if (ks_resize(s, s->l + 1) < 0)
  		return EOF;
  	s->s[s->l++] = c;
  	return 1;
  }
  
  static inline int kputsn_(const void *p, size_t l, kstring_t *s)
  {
  	size_t new_sz = s->l + l;
  	if (new_sz < s->l || ks_resize(s, new_sz ? new_sz : 1) < 0)
  		return EOF;
  	memcpy(s->s + s->l, p, l);
  	s->l += l;
  	return l;
  }
  
  static inline int kputuw(unsigned x, kstring_t *s)
  {
  #if HAVE___BUILTIN_CLZ && UINT_MAX == 4294967295U
      static const unsigned int kputuw_num_digits[32] = {
          10, 10, 10,  9,  9,  9,  8,  8,
          8,   7,  7,  7,  7,  6,  6,  6,
          5,   5,  5,  4,  4,  4,  4,  3,
          3,   3,  2,  2,  2,  1,  1,  1
      };
      static const unsigned int kputuw_thresholds[32] = {
          0,        0, 1000000000U, 0,       0, 100000000U,   0,      0,
          10000000, 0,          0,  0, 1000000,         0,    0, 100000,
          0,        0,      10000,  0,       0,         0, 1000,      0,
          0,      100,          0,  0,      10,         0,    0,      0
      };
  #else
      uint64_t m;
  #endif
      static const char kputuw_dig2r[] =
          "00010203040506070809"
          "10111213141516171819"
          "20212223242526272829"
          "30313233343536373839"
          "40414243444546474849"
          "50515253545556575859"
          "60616263646566676869"
          "70717273747576777879"
          "80818283848586878889"
          "90919293949596979899";
      unsigned int l, j;
      char *cp;
  
      // Trivial case - also prevents __builtin_clz(0), which is undefined
      if (x < 10) {
          if (ks_resize(s, s->l + 2) < 0)
              return EOF;
          s->s[s->l++] = '0'+x;
          s->s[s->l] = 0;
          return 0;
      }
  
      // Find out how many digits are to be printed.
  #if HAVE___BUILTIN_CLZ && UINT_MAX == 4294967295U
      /*
       * Table method - should be quick if clz can be done in hardware.
       * Find the most significant bit of the value to print and look
       * up in a table to find out how many decimal digits are needed.
       * This number needs to be adjusted by 1 for cases where the decimal
       * length could vary for a given number of bits (for example,
       * a four bit number could be between 8 and 15).
       */
  
      l = __builtin_clz(x);
      l = kputuw_num_digits[l] - (x < kputuw_thresholds[l]);
  #else
      // Fallback for when clz is not available
      m = 1;
      l = 0;
      do {
          l++;
          m *= 10;
      } while (x >= m);
  #endif
  
      if (ks_resize(s, s->l + l + 2) < 0)
          return EOF;
  
      // Add digits two at a time
      j = l;
      cp = s->s + s->l;
      while (x >= 10) {
          const char *d = &kputuw_dig2r[2*(x%100)];
          x /= 100;
          memcpy(&cp[j-=2], d, 2);
      }
  
      // Last one (if necessary).  We know that x < 10 by now.
      if (j == 1)
          cp[0] = x + '0';
  
      s->l += l;
      s->s[s->l] = 0;
      return 0;
  }
  
  static inline int kputw(int c, kstring_t *s)
  {
      unsigned int x = c;
      if (c < 0) {
          x = -x;
          if (ks_resize(s, s->l + 3) < 0)
              return EOF;
          s->s[s->l++] = '-';
      }
  
      return kputuw(x, s);
  }
  
  static inline int kputll(long long c, kstring_t *s)
  {
  	char buf[32];
  	int i, l = 0;
  	unsigned long long x = c;
  	if (c < 0) x = -x;
  	do { buf[l++] = x%10 + '0'; x /= 10; } while (x > 0);
  	if (c < 0) buf[l++] = '-';
  	if (ks_resize(s, s->l + l + 2) < 0)
  		return EOF;
  	for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];
  	s->s[s->l] = 0;
  	return 0;
  }
  
  static inline int kputl(long c, kstring_t *s) {
      return kputll(c, s);
  }
  
  #define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
  #define KS_SEP_TAB   1 // isspace() && !' '
  #define KS_SEP_LINE  2 // line separator: "\n" (Unix) or "\r\n" (Windows)
  #define KS_SEP_MAX   2
  
  /*
   * Returns 's' split by delimiter, with *n being the number of components;
   *         NULL on failue.
   */
  static inline int *ksplit(kstring_t *s, int delimiter, int *n)
  {
  	int max = 0, *offsets = 0;
  	*n = ksplit_core(s->s, delimiter, &max, &offsets);
  	return offsets;
  }
  
  #endif
  