/src/htslib/htslib/ksort.h

Source
/* The MIT License

   Copyright (c) 2008, 2012-2013, 2017-2019 Genome Research Ltd (GRL).

   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.
*/

/* Contact: Heng Li <lh3@sanger.ac.uk> */

/*
  2012-12-11 (0.1.4):

    * Defined __ks_insertsort_##name as static to compile with C99.

  2008-11-16 (0.1.4):

    * Fixed a bug in introsort() that happens in rare cases.

  2008-11-05 (0.1.3):

    * Fixed a bug in introsort() for complex comparisons.

  * Fixed a bug in mergesort(). The previous version is not stable.

  2008-09-15 (0.1.2):

  * Accelerated introsort. On my Mac (not on another Linux machine),
    my implementation is as fast as the C++ standard library's sort()
    on random input.

  * Added combsort and in introsort, switch to combsort if the
    recursion is too deep.

  2008-09-13 (0.1.1):

  * Added k-small algorithm

  2008-09-05 (0.1.0):

  * Initial version

*/

#ifndef AC_KSORT_H
#define AC_KSORT_H

#include <stdlib.h>
#include <string.h>
#include "hts_defs.h"

#ifndef klib_unused
#if (defined __clang__ && __clang_major__ >= 3) || (defined __GNUC__ && __GNUC__ >= 3)
#define klib_unused __attribute__ ((__unused__))
#else
#define klib_unused
#endif
#endif /* klib_unused */

#ifdef __cplusplus
extern "C" {
#endif

// Use our own drand48() symbol (used by ks_shuffle) to avoid portability
// problems on Windows.  Don't include htslib/hts_os.h for this as it
// may not get on with older attempts to fix this in code that includes
// this file.
HTSLIB_EXPORT
extern double hts_drand48(void);

typedef struct {
  void *left, *right;
  int depth;
} ks_isort_stack_t;

#define KSORT_SWAP(type_t, a, b) { type_t t=(a); (a)=(b); (b)=t; }

#define KSORT_INIT(name, type_t, __sort_lt) KSORT_INIT_(_ ## name, , type_t, __sort_lt)
#define KSORT_INIT_STATIC(name, type_t, __sort_lt)  KSORT_INIT_(_ ## name, static klib_unused, type_t, __sort_lt)
#define KSORT_INIT2(name, SCOPE, type_t, __sort_lt) KSORT_INIT_(_ ## name, SCOPE, type_t, __sort_lt)

#define KSORT_INIT_(name, SCOPE, type_t, __sort_lt)           \
  SCOPE int ks_mergesort##name(size_t n, type_t array[], type_t temp[]) \
  {                                 \
    type_t *a2[2], *a, *b;                      \
    int curr, shift;                        \
                                    \
    a2[0] = array;                          \
    a2[1] = temp? temp : (type_t*)malloc(sizeof(type_t) * n);   \
    for (curr = 0, shift = 0; (1ul<<shift) < n; ++shift) {      \
      a = a2[curr]; b = a2[1-curr];               \
      if (shift == 0) {                     \
        type_t *p = b, *i, *eb = a + n;             \
        for (i = a; i < eb; i += 2) {             \
          if (i == eb - 1) *p++ = *i;             \
          else {                        \
            if (__sort_lt(*(i+1), *i)) {          \
              *p++ = *(i+1); *p++ = *i;         \
            } else {                    \
              *p++ = *i; *p++ = *(i+1);         \
            }                       \
          }                         \
        }                           \
      } else {                          \
        size_t i, step = 1ul<<shift;              \
        for (i = 0; i < n; i += step<<1) {            \
          type_t *p, *j, *k, *ea, *eb;            \
          if (n < i + step) {                 \
            ea = a + n; eb = a;               \
          } else {                      \
            ea = a + i + step;                \
            eb = a + (n < i + (step<<1)? n : i + (step<<1)); \
          }                         \
          j = a + i; k = a + i + step; p = b + i;       \
          while (j < ea && k < eb) {              \
            if (__sort_lt(*k, *j)) *p++ = *k++;       \
            else *p++ = *j++;               \
          }                         \
          while (j < ea) *p++ = *j++;             \
          while (k < eb) *p++ = *k++;             \
        }                           \
      }                             \
      curr = 1 - curr;                      \
    }                               \
    if (curr == 1) {                        \
      type_t *p = a2[0], *i = a2[1], *eb = array + n;       \
      for (; p < eb; ++i) *p++ = *i;                \
    }                               \
    if (temp == 0) free(a2[1]);                   \
    return 0;                             \
  }                                  \
  SCOPE void ks_heapadjust##name(size_t i, size_t n, type_t l[])    \
  {                                 \
    size_t k = i;                         \
    type_t tmp = l[i];                        \
    while ((k = (k << 1) + 1) < n) {                \
      if (k != n - 1 && __sort_lt(l[k], l[k+1])) ++k;       \
      if (__sort_lt(l[k], tmp)) break;              \
      l[i] = l[k]; i = k;                     \
    }                               \
    l[i] = tmp;                           \
  }                                  \
  SCOPE void ks_heapmake##name(size_t lsize, type_t l[])        \
  {                                 \
    size_t i;                           \
    for (i = (lsize >> 1) - 1; i != (size_t)(-1); --i)        \
      ks_heapadjust##name(i, lsize, l);             \
  }                                  \
  SCOPE void ks_heapsort##name(size_t lsize, type_t l[])        \
  {                                 \
    size_t i;                           \
    for (i = lsize - 1; i > 0; --i) {               \
      type_t tmp;                         \
      tmp = *l; *l = l[i]; l[i] = tmp; ks_heapadjust##name(0, i, l); \
    }                               \
  }                                  \
  static inline void __ks_insertsort##name(type_t *s, type_t *t)    \
  {                                 \
    type_t *i, *j, swap_tmp;                    \
    for (i = s + 1; i < t; ++i)                   \
      for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) {     \
        swap_tmp = *j; *j = *(j-1); *(j-1) = swap_tmp;      \
      }                              \
  }                                  \
  SCOPE void ks_combsort##name(size_t n, type_t a[])          \
  {                                 \
    const double shrink_factor = 1.2473309501039786540366528676643; \
    int do_swap;                          \
    size_t gap = n;                         \
    type_t tmp, *i, *j;                       \
    do {                             \
      if (gap > 2) {                       \
        gap = (size_t)(gap / shrink_factor);          \
        if (gap == 9 || gap == 10) gap = 11;         \
      }                             \
      do_swap = 0;                        \
      for (i = a; i < a + n - gap; ++i) {             \
        j = i + gap;                      \
        if (__sort_lt(*j, *i)) {               \
          tmp = *i; *i = *j; *j = tmp;            \
          do_swap = 1;                    \
        }                            \
      }                             \
    } while (do_swap || gap > 2);                  \
    if (gap != 1) __ks_insertsort##name(a, a + n);         \
  }                                  \
  SCOPE int ks_introsort##name(size_t n, type_t a[])          \
  {                                 \
    int d;                              \
    ks_isort_stack_t *top, *stack;                  \
    type_t rp, swap_tmp;                      \
    type_t *s, *t, *i, *j, *k;                    \
                                    \
    if (n < 1) return 0;                       \
    else if (n == 2) {                       \
      if (__sort_lt(a[1], a[0])) { swap_tmp = a[0]; a[0] = a[1]; a[1] = swap_tmp; } \
      return 0;                           \
    }                               \
    for (d = 2; 1ul<<d < n; ++d);                  \
    stack = (ks_isort_stack_t*)malloc(sizeof(ks_isort_stack_t) * ((sizeof(size_t)*d)+2)); \
    top = stack; s = a; t = a + (n-1); d <<= 1;           \
    while (1) {                           \
      if (s < t) {                       \
        if (--d == 0) {                     \
          ks_combsort##name(t - s + 1, s);         \
          t = s;                        \
          continue;                     \
        }                           \
        i = s; j = t; k = i + ((j-i)>>1) + 1;         \
        if (__sort_lt(*k, *i)) {               \
          if (__sort_lt(*k, *j)) k = j;           \
        } else k = __sort_lt(*j, *i)? i : j;         \
        rp = *k;                        \
        if (k != t) { swap_tmp = *k; *k = *t; *t = swap_tmp; }  \
        for (;;) {                       \
          do ++i; while (__sort_lt(*i, rp));          \
          do --j; while (i <= j && __sort_lt(rp, *j));    \
          if (j <= i) break;                 \
          swap_tmp = *i; *i = *j; *j = swap_tmp;        \
        }                            \
        swap_tmp = *i; *i = *t; *t = swap_tmp;          \
        if (i-s > t-i) {                   \
          if (i-s > 16) { top->left = s; top->right = i-1; top->depth = d; ++top; } \
          s = t-i > 16? i+1 : t;               \
        } else {                       \
          if (t-i > 16) { top->left = i+1; top->right = t; top->depth = d; ++top; } \
          t = i-s > 16? i-1 : s;               \
        }                           \
      } else {                         \
        if (top == stack) {                   \
          free(stack);                    \
          __ks_insertsort##name(a, a+n);           \
          return 0;                       \
        } else { --top; s = (type_t*)top->left; t = (type_t*)top->right; d = top->depth; } \
      }                             \
    }                               \
    return 0;                             \
  }                                  \
  /* This function is adapted from: http://ndevilla.free.fr/median/ */ \
  /* 0 <= kk < n */                         \
  SCOPE type_t ks_ksmall##name(size_t n, type_t arr[], size_t kk)   \
  {                                 \
    type_t *low, *high, *k, *ll, *hh, *mid;             \
    low = arr; high = arr + n - 1; k = arr + kk;          \
    for (;;) {                            \
      if (high <= low) return *k;                 \
      if (high == low + 1) {                    \
        if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
        return *k;                        \
      }                             \
      mid = low + (high - low) / 2;               \
      if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \
      if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
      if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low);  \
      KSORT_SWAP(type_t, *mid, *(low+1));             \
      ll = low + 1; hh = high;                  \
      for (;;) {                          \
        do ++ll; while (__sort_lt(*ll, *low));          \
        do --hh; while (__sort_lt(*low, *hh));          \
        if (hh < ll) break;                   \
        KSORT_SWAP(type_t, *ll, *hh);             \
      }                             \
      KSORT_SWAP(type_t, *low, *hh);                \
      if (hh <= k) low = ll;                    \
      if (hh >= k) high = hh - 1;                 \
    }                               \
  }                                  \
  SCOPE void ks_shuffle##name(size_t n, type_t a[])         \
  {                                 \
    int i, j;                           \
    for (i = n; i > 1; --i) {                   \
      type_t tmp;                         \
      j = (int)(hts_drand48() * i);               \
      tmp = a[j]; a[j] = a[i-1]; a[i-1] = tmp;          \
    }                               \
  }

#define ks_mergesort(name, n, a, t) ks_mergesort_##name(n, a, t)
#define ks_introsort(name, n, a) ks_introsort_##name(n, a)
#define ks_combsort(name, n, a) ks_combsort_##name(n, a)
#define ks_heapsort(name, n, a) ks_heapsort_##name(n, a)
#define ks_heapmake(name, n, a) ks_heapmake_##name(n, a)
#define ks_heapadjust(name, i, n, a) ks_heapadjust_##name(i, n, a)
#define ks_ksmall(name, n, a, k) ks_ksmall_##name(n, a, k)
#define ks_shuffle(name, n, a) ks_shuffle_##name(n, a)

#define ks_lt_generic(a, b) ((a) < (b))
#define ks_lt_str(a, b) (strcmp((a), (b)) < 0)

typedef const char *ksstr_t;

#define KSORT_INIT_GENERIC(type_t) KSORT_INIT_(_ ## type_t, , type_t, ks_lt_generic)
#define KSORT_INIT_STR KSORT_INIT(str, ksstr_t, ks_lt_str)

#define KSORT_INIT_STATIC_GENERIC(type_t) KSORT_INIT_(_ ## type_t, static klib_unused, type_t, ks_lt_generic)
#define KSORT_INIT_STATIC_STR KSORT_INIT_STATIC(str, ksstr_t, ks_lt_str)

#define KSORT_INIT2_GENERIC(type_t, SCOPE) KSORT_INIT_(_ ## type_t, SCOPE, type_t, ks_lt_generic)
#define KSORT_INIT2_STR KSORT_INIT2(str, SCOPE, ksstr_t, ks_lt_str)

#ifdef __cplusplus
}
#endif

#endif

Coverage Report

Created: 2025-11-11 06:39

Line	Count	Source
1		/* The MIT License
2
3		Copyright (c) 2008, 2012-2013, 2017-2019 Genome Research Ltd (GRL).
4
5		Permission is hereby granted, free of charge, to any person obtaining
6		a copy of this software and associated documentation files (the
7		"Software"), to deal in the Software without restriction, including
8		without limitation the rights to use, copy, modify, merge, publish,
9		distribute, sublicense, and/or sell copies of the Software, and to
10		permit persons to whom the Software is furnished to do so, subject to
11		the following conditions:
12
13		The above copyright notice and this permission notice shall be
14		included in all copies or substantial portions of the Software.
15
16		THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
17		EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
18		MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
19		NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
20		BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
21		ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
22		CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
23		SOFTWARE.
24		*/
25
26		/* Contact: Heng Li <lh3@sanger.ac.uk> */
27
28		/*
29		2012-12-11 (0.1.4):
30
31		* Defined __ks_insertsort_##name as static to compile with C99.
32
33		2008-11-16 (0.1.4):
34
35		* Fixed a bug in introsort() that happens in rare cases.
36
37		2008-11-05 (0.1.3):
38
39		* Fixed a bug in introsort() for complex comparisons.
40
41		* Fixed a bug in mergesort(). The previous version is not stable.
42
43		2008-09-15 (0.1.2):
44
45		* Accelerated introsort. On my Mac (not on another Linux machine),
46		my implementation is as fast as the C++ standard library's sort()
47		on random input.
48
49		* Added combsort and in introsort, switch to combsort if the
50		recursion is too deep.
51
52		2008-09-13 (0.1.1):
53
54		* Added k-small algorithm
55
56		2008-09-05 (0.1.0):
57
58		* Initial version
59
60		*/
61
62		#ifndef AC_KSORT_H
63		#define AC_KSORT_H
64
65		#include <stdlib.h>
66		#include <string.h>
67		#include "hts_defs.h"
68
69		#ifndef klib_unused
70		#if (defined __clang__ && __clang_major__ >= 3) \|\| (defined __GNUC__ && __GNUC__ >= 3)
71		#define klib_unused __attribute__ ((__unused__))
72		#else
73		#define klib_unused
74		#endif
75		#endif /* klib_unused */
76
77		#ifdef __cplusplus
78		extern "C" {
79		#endif
80
81		// Use our own drand48() symbol (used by ks_shuffle) to avoid portability
82		// problems on Windows. Don't include htslib/hts_os.h for this as it
83		// may not get on with older attempts to fix this in code that includes
84		// this file.
85		HTSLIB_EXPORT
86		extern double hts_drand48(void);
87
88		typedef struct {
89		void left, right;
90		int depth;
91		} ks_isort_stack_t;
92
93		#define KSORT_SWAP(type_t, a, b) { type_t t=(a); (a)=(b); (b)=t; }
94
95		#define KSORT_INIT(name, type_t, __sort_lt) KSORT_INIT_(_ ## name, , type_t, __sort_lt)
96		#define KSORT_INIT_STATIC(name, type_t, __sort_lt) KSORT_INIT_(_ ## name, static klib_unused, type_t, __sort_lt)
97		#define KSORT_INIT2(name, SCOPE, type_t, __sort_lt) KSORT_INIT_(_ ## name, SCOPE, type_t, __sort_lt)
98
99		#define KSORT_INIT_(name, SCOPE, type_t, __sort_lt) \
100		SCOPE int ks_mergesort##name(size_t n, type_t array[], type_t temp[]) \
101	0	{ \
102	0	type_t a2[2], a, *b; \
103	0	int curr, shift; \
104	0	\
105	0	a2[0] = array; \
106	0	a2[1] = temp? temp : (type_t)malloc(sizeof(type_t) n); \
107	0	for (curr = 0, shift = 0; (1ul<<shift) < n; ++shift) { \
108	0	a = a2[curr]; b = a2[1-curr]; \
109	0	if (shift == 0) { \
110	0	type_t p = b, i, *eb = a + n; \
111	0	for (i = a; i < eb; i += 2) { \
112	0	if (i == eb - 1) p++ = i; \
113	0	else { \
114	0	if (__sort_lt((i+1), i)) { \
115	0	p++ = (i+1); p++ = i; \
116	0	} else { \
117	0	p++ = i; p++ = (i+1); \
118	0	} \
119	0	} \
120	0	} \
121	0	} else { \
122	0	size_t i, step = 1ul<<shift; \
123	0	for (i = 0; i < n; i += step<<1) { \
124	0	type_t p, j, k, ea, *eb; \
125	0	if (n < i + step) { \
126	0	ea = a + n; eb = a; \
127	0	} else { \
128	0	ea = a + i + step; \
129	0	eb = a + (n < i + (step<<1)? n : i + (step<<1)); \
130	0	} \
131	0	j = a + i; k = a + i + step; p = b + i; \
132	0	while (j < ea && k < eb) { \
133	0	if (__sort_lt(k, j)) p++ = k++; \
134	0	else p++ = j++; \
135	0	} \
136	0	while (j < ea) p++ = j++; \
137	0	while (k < eb) p++ = k++; \
138	0	} \
139	0	} \
140	0	curr = 1 - curr; \
141	0	} \
142	0	if (curr == 1) { \
143	0	type_t p = a2[0], i = a2[1], *eb = array + n; \
144	0	for (; p < eb; ++i) p++ = i; \
145	0	} \
146	0	if (temp == 0) free(a2[1]); \
147	0	return 0; \
148	0	} \ Unexecuted instantiation: hts.c:ks_mergesort__off Unexecuted instantiation: hts.c:ks_mergesort__off_max
149		SCOPE void ks_heapadjust##name(size_t i, size_t n, type_t l[]) \
150	0	{ \
151	0	size_t k = i; \
152	0	type_t tmp = l[i]; \
153	0	while ((k = (k << 1) + 1) < n) { \
154	0	if (k != n - 1 && __sort_lt(l[k], l[k+1])) ++k; \
155	0	if (__sort_lt(l[k], tmp)) break; \
156	0	l[i] = l[k]; i = k; \
157	0	} \
158	0	l[i] = tmp; \
159	0	} \ Unexecuted instantiation: hts.c:ks_heapadjust__off Unexecuted instantiation: hts.c:ks_heapadjust__off_max
160		SCOPE void ks_heapmake##name(size_t lsize, type_t l[]) \
161	0	{ \
162	0	size_t i; \
163	0	for (i = (lsize >> 1) - 1; i != (size_t)(-1); --i) \
164	0	ks_heapadjust##name(i, lsize, l); \
165	0	} \ Unexecuted instantiation: hts.c:ks_heapmake__off Unexecuted instantiation: hts.c:ks_heapmake__off_max
166		SCOPE void ks_heapsort##name(size_t lsize, type_t l[]) \
167	0	{ \
168	0	size_t i; \
169	0	for (i = lsize - 1; i > 0; --i) { \
170	0	type_t tmp; \
171	0	tmp = l; l = l[i]; l[i] = tmp; ks_heapadjust##name(0, i, l); \
172	0	} \
173	0	} \ Unexecuted instantiation: hts.c:ks_heapsort__off Unexecuted instantiation: hts.c:ks_heapsort__off_max
174		static inline void __ks_insertsort##name(type_t s, type_t t) \
175	0	{ \
176	0	type_t i, j, swap_tmp; \
177	0	for (i = s + 1; i < t; ++i) \
178	0	for (j = i; j > s && __sort_lt(j, (j-1)); --j) { \
179	0	swap_tmp = j; j = (j-1); (j-1) = swap_tmp; \
180	0	} \
181	0	} \ Unexecuted instantiation: hts.c:__ks_insertsort__off Unexecuted instantiation: hts.c:__ks_insertsort__off_max
182		SCOPE void ks_combsort##name(size_t n, type_t a[]) \
183	0	{ \
184	0	const double shrink_factor = 1.2473309501039786540366528676643; \
185	0	int do_swap; \
186	0	size_t gap = n; \
187	0	type_t tmp, i, j; \
188	0	do { \
189	0	if (gap > 2) { \
190	0	gap = (size_t)(gap / shrink_factor); \
191	0	if (gap == 9 \|\| gap == 10) gap = 11; \
192	0	} \
193	0	do_swap = 0; \
194	0	for (i = a; i < a + n - gap; ++i) { \
195	0	j = i + gap; \
196	0	if (__sort_lt(j, i)) { \
197	0	tmp = i; i = j; j = tmp; \
198	0	do_swap = 1; \
199	0	} \
200	0	} \
201	0	} while (do_swap \|\| gap > 2); \
202	0	if (gap != 1) __ks_insertsort##name(a, a + n); \
203	0	} \ Unexecuted instantiation: hts.c:ks_combsort__off Unexecuted instantiation: hts.c:ks_combsort__off_max
204		SCOPE int ks_introsort##name(size_t n, type_t a[]) \
205	0	{ \
206	0	int d; \
207	0	ks_isort_stack_t top, stack; \
208	0	type_t rp, swap_tmp; \
209	0	type_t s, t, i, j, *k; \
210	0	\
211	0	if (n < 1) return 0; \
212	0	else if (n == 2) { \
213	0	if (__sort_lt(a[1], a[0])) { swap_tmp = a[0]; a[0] = a[1]; a[1] = swap_tmp; } \
214	0	return 0; \
215	0	} \
216	0	for (d = 2; 1ul<<d < n; ++d); \
217	0	stack = (ks_isort_stack_t)malloc(sizeof(ks_isort_stack_t) ((sizeof(size_t)*d)+2)); \
218	0	top = stack; s = a; t = a + (n-1); d <<= 1; \
219	0	while (1) { \
220	0	if (s < t) { \
221	0	if (--d == 0) { \
222	0	ks_combsort##name(t - s + 1, s); \
223	0	t = s; \
224	0	continue; \
225	0	} \
226	0	i = s; j = t; k = i + ((j-i)>>1) + 1; \
227	0	if (__sort_lt(k, i)) { \
228	0	if (__sort_lt(k, j)) k = j; \
229	0	} else k = __sort_lt(j, i)? i : j; \
230	0	rp = *k; \
231	0	if (k != t) { swap_tmp = k; k = t; t = swap_tmp; } \
232	0	for (;;) { \
233	0	do ++i; while (__sort_lt(*i, rp)); \
234	0	do --j; while (i <= j && __sort_lt(rp, *j)); \
235	0	if (j <= i) break; \
236	0	swap_tmp = i; i = j; j = swap_tmp; \
237	0	} \
238	0	swap_tmp = i; i = t; t = swap_tmp; \
239	0	if (i-s > t-i) { \
240	0	if (i-s > 16) { top->left = s; top->right = i-1; top->depth = d; ++top; } \
241	0	s = t-i > 16? i+1 : t; \
242	0	} else { \
243	0	if (t-i > 16) { top->left = i+1; top->right = t; top->depth = d; ++top; } \
244	0	t = i-s > 16? i-1 : s; \
245	0	} \
246	0	} else { \
247	0	if (top == stack) { \
248	0	free(stack); \
249	0	__ks_insertsort##name(a, a+n); \
250	0	return 0; \
251	0	} else { --top; s = (type_t)top->left; t = (type_t)top->right; d = top->depth; } \
252	0	} \
253	0	} \
254	0	return 0; \
255	0	} \ Unexecuted instantiation: hts.c:ks_introsort__off Unexecuted instantiation: hts.c:ks_introsort__off_max
256		/* This function is adapted from: http://ndevilla.free.fr/median/ */ \
257		/* 0 <= kk < n */ \
258		SCOPE type_t ks_ksmall##name(size_t n, type_t arr[], size_t kk) \
259	0	{ \
260	0	type_t low, high, k, ll, hh, mid; \
261	0	low = arr; high = arr + n - 1; k = arr + kk; \
262	0	for (;;) { \
263	0	if (high <= low) return *k; \
264	0	if (high == low + 1) { \
265	0	if (__sort_lt(high, low)) KSORT_SWAP(type_t, low, high); \
266	0	return *k; \
267	0	} \
268	0	mid = low + (high - low) / 2; \
269	0	if (__sort_lt(high, mid)) KSORT_SWAP(type_t, mid, high); \
270	0	if (__sort_lt(high, low)) KSORT_SWAP(type_t, low, high); \
271	0	if (__sort_lt(low, mid)) KSORT_SWAP(type_t, mid, low); \
272	0	KSORT_SWAP(type_t, mid, (low+1)); \
273	0	ll = low + 1; hh = high; \
274	0	for (;;) { \
275	0	do ++ll; while (__sort_lt(ll, low)); \
276	0	do --hh; while (__sort_lt(low, hh)); \
277	0	if (hh < ll) break; \
278	0	KSORT_SWAP(type_t, ll, hh); \
279	0	} \
280	0	KSORT_SWAP(type_t, low, hh); \
281	0	if (hh <= k) low = ll; \
282	0	if (hh >= k) high = hh - 1; \
283	0	} \
284	0	} \ Unexecuted instantiation: hts.c:ks_ksmall__off Unexecuted instantiation: hts.c:ks_ksmall__off_max
285		SCOPE void ks_shuffle##name(size_t n, type_t a[]) \
286	0	{ \
287	0	int i, j; \
288	0	for (i = n; i > 1; --i) { \
289	0	type_t tmp; \
290	0	j = (int)(hts_drand48() * i); \
291	0	tmp = a[j]; a[j] = a[i-1]; a[i-1] = tmp; \
292	0	} \
293	0	} Unexecuted instantiation: hts.c:ks_shuffle__off Unexecuted instantiation: hts.c:ks_shuffle__off_max
294
295		#define ks_mergesort(name, n, a, t) ks_mergesort_##name(n, a, t)
296	0	#define ks_introsort(name, n, a) ks_introsort_##name(n, a)
297		#define ks_combsort(name, n, a) ks_combsort_##name(n, a)
298		#define ks_heapsort(name, n, a) ks_heapsort_##name(n, a)
299		#define ks_heapmake(name, n, a) ks_heapmake_##name(n, a)
300		#define ks_heapadjust(name, i, n, a) ks_heapadjust_##name(i, n, a)
301		#define ks_ksmall(name, n, a, k) ks_ksmall_##name(n, a, k)
302		#define ks_shuffle(name, n, a) ks_shuffle_##name(n, a)
303
304		#define ks_lt_generic(a, b) ((a) < (b))
305		#define ks_lt_str(a, b) (strcmp((a), (b)) < 0)
306
307		typedef const char *ksstr_t;
308
309		#define KSORT_INIT_GENERIC(type_t) KSORT_INIT_(_ ## type_t, , type_t, ks_lt_generic)
310		#define KSORT_INIT_STR KSORT_INIT(str, ksstr_t, ks_lt_str)
311
312		#define KSORT_INIT_STATIC_GENERIC(type_t) KSORT_INIT_(_ ## type_t, static klib_unused, type_t, ks_lt_generic)
313		#define KSORT_INIT_STATIC_STR KSORT_INIT_STATIC(str, ksstr_t, ks_lt_str)
314
315		#define KSORT_INIT2_GENERIC(type_t, SCOPE) KSORT_INIT_(_ ## type_t, SCOPE, type_t, ks_lt_generic)
316		#define KSORT_INIT2_STR KSORT_INIT2(str, SCOPE, ksstr_t, ks_lt_str)
317
318		#ifdef __cplusplus
319		}
320		#endif
321
322		#endif