New upstream version 1.3 (ba538534) · Commits · Debian Med / seqtk

Makefile

+4 −0

Original line number	Diff line number	Diff line
		CC=gcc
		CFLAGS=-g -Wall -O2 -Wno-unused-function
		BINDIR=/usr/local/bin

		all:seqtk

		seqtk:seqtk.c khash.h kseq.h
		$(CC) $(CFLAGS) seqtk.c -o $@ -lz -lm

		install:all
		install seqtk $(BINDIR)

		clean:
		rm -fr gmon.out .o ext/.o a.out seqtk trimadap ~ .a .dSYM session

kseq.h

+113 −105

Original line number	Diff line number	Diff line
		@@ -23,7 +23,7 @@
		SOFTWARE.
		*/

		/* Last Modified: 05MAR2012 */
		/* Last Modified: 2017-02-11 */

		#ifndef AC_KSEQ_H
		#define AC_KSEQ_H
		@@ -44,6 +44,7 @@
		type_t f; \
		} kstream_t;

		#define ks_err(ks) ((ks)->end < 0)
		#define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
		#define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)

		@@ -66,11 +67,13 @@
		#define __KS_GETC(__read, __bufsize) \
		static inline int ks_getc(kstream_t *ks) \
		{ \
		if (ks->is_eof && ks->begin >= ks->end) return -1; \
		if (ks_err(ks)) return -3; \
		if (ks_eof(ks)) return -1; \
		if (ks->begin >= ks->end) { \
		ks->begin = 0; \
		ks->end = __read(ks->f, ks->buf, __bufsize); \
		if (ks->end == 0) { ks->is_eof = 1; return -1; } \
		else if (ks->end < 0) { ks->is_eof = 1; return -3; } \
		} \
		return (int)ks->buf[ks->begin++]; \
		}
		@@ -95,11 +98,13 @@ typedef struct __kstring_t {
		str->l = append? str->l : 0; \
		for (;;) { \
		int i; \
		if (ks_err(ks)) return -3; \
		if (ks->begin >= ks->end) { \
		if (!ks->is_eof) { \
		ks->begin = 0; \
		ks->end = __read(ks->f, ks->buf, __bufsize); \
		if (ks->end == 0) { ks->is_eof = 1; break; } \
		if (ks->end == -1) { ks->is_eof = 1; return -3; } \
		} else break; \
		} \
		if (delimiter == KS_SEP_LINE) { \
		@@ -167,25 +172,26 @@ typedef struct __kstring_t {
		>=0 length of the sequence (normal)
		-1 end-of-file
		-2 truncated quality string
		-3 error reading stream
		*/
		#define __KSEQ_READ(SCOPE) \
		SCOPE int kseq_read(kseq_t *seq) \
		{ \
		int c; \
		int c,r; \
		kstream_t *ks = seq->f; \
		if (seq->last_char == 0) { /* then jump to the next header line */ \
		while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
		if (c == -1) return -1; /* end of file */ \
		while ((c = ks_getc(ks)) >= 0 && c != '>' && c != '@'); \
		if (c < 0) return c; /* end of file or error*/ \
		seq->last_char = c; \
		} /* else: the first header char has been read in the previous call */ \
		seq->comment.l = seq->seq.l = seq->qual.l = 0; /* reset all members */ \
		if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \
		if ((r=ks_getuntil(ks, 0, &seq->name, &c)) < 0) return r; /* normal exit: EOF or error */ \
		if (c != '\n') ks_getuntil(ks, KS_SEP_LINE, &seq->comment, 0); /* read FASTA/Q comment */ \
		if (seq->seq.s == 0) { /* we can do this in the loop below, but that is slower */ \
		seq->seq.m = 256; \
		seq->seq.s = (char*)malloc(seq->seq.m); \
		} \
		while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
		while ((c = ks_getc(ks)) >= 0 && c != '>' && c != '+' && c != '@') { \
		if (c == '\n') continue; /* skip empty lines */ \
		seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \
		ks_getuntil2(ks, KS_SEP_LINE, &seq->seq, 0, 1); /* read the rest of the line */ \
		@@ -197,14 +203,16 @@ typedef struct __kstring_t {
		seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
		} \
		seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \
		if (c != '+') return seq->seq.l; /* FASTA */ \
		seq->is_fastq = (c == '+'); \
		if (!seq->is_fastq) return seq->seq.l; /* FASTA */ \
		if (seq->qual.m < seq->seq.m) { /* allocate memory for qual in case insufficient */ \
		seq->qual.m = seq->seq.m; \
		seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
		} \
		while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
		while ((c = ks_getc(ks)) >= 0 && c != '\n'); /* skip the rest of '+' line */ \
		if (c == -1) return -2; /* error: no quality string */ \
		while (ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \
		while ((c = ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l)); \
		if (c == -3) return -3; /* stream error */ \
		seq->last_char = 0; /* we have not come to the next header line */ \
		if (seq->seq.l != seq->qual.l) return -2; /* error: qual string is of a different length */ \
		return seq->seq.l; \
		@@ -213,7 +221,7 @@ typedef struct __kstring_t {
		#define __KSEQ_TYPE(type_t) \
		typedef struct { \
		kstring_t name, comment, seq, qual; \
		int last_char; \
		int last_char, is_fastq; \
		kstream_t *f; \
		} kseq_t;

ksort.h

deleted100644 → 0

+0 −298

Original line number	Diff line number	Diff line
		/* The MIT License

		Copyright (c) 2008, 2011 Attractive Chaos <attractor@live.co.uk>

		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.
		*/

		/*
		2011-04-10 (0.1.6):

		* Added sample

		2011-03 (0.1.5):

		* Added shuffle/permutation

		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 std::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>

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

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

		#define KSORT_INIT(name, type_t, __sort_lt) \
		void 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]); \
		} \
		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; \
		} \
		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); \
		} \
		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; \
		} \
		} \
		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); \
		} \
		void 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; \
		else if (n == 2) { \
		if (__sort_lt(a[1], a[0])) { swap_tmp = a[0]; a[0] = a[1]; a[1] = swap_tmp; } \
		return; \
		} \
		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; \
		} else { --top; s = (type_t)top->left; t = (type_t)top->right; d = top->depth; } \
		} \
		} \
		} \
		/* This function is adapted from: http://ndevilla.free.fr/median/ */ \
		/* 0 <= kk < n */ \
		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; \
		} \
		} \
		void ks_shuffle_##name(size_t n, type_t a[]) \
		{ \
		int i, j; \
		for (i = n; i > 1; --i) { \
		type_t tmp; \
		j = (int)(drand48() * i); \
		tmp = a[j]; a[j] = a[i-1]; a[i-1] = tmp; \
		} \
		} \
		void ks_sample_##name(size_t n, size_t r, type_t a[]) /* FIXME: NOT TESTED!!! */ \
		{ /* reference: http://code.activestate.com/recipes/272884/ */ \
		int i, k, pop = n; \
		for (i = (int)r, k = 0; i >= 0; --i) { \
		double z = 1., x = drand48(); \
		type_t tmp; \
		while (x < z) z -= z * i / (pop--); \
		if (k != n - pop - 1) tmp = a[k], a[k] = a[n-pop-1], a[n-pop-1] = tmp; \
		++k; \
		} \
		}

		#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)

		#endif

kstring.h

deleted100644 → 0

+0 −169

Original line number	Diff line number	Diff line
		/* The MIT License

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

		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 <stdint.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 KSTRING_T
		#define KSTRING_T kstring_t
		typedef struct __kstring_t {
		uint32_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

		int ksprintf(kstring_t s, const char fmt, ...);
		int ksprintf_fast(kstring_t s, const char fmt, ...);
		int ksplit_core(char s, int delimiter, int _max, int **_offsets);
		char kstrstr(const char str, const char pat, int *_prep);
		char kstrnstr(const char str, const char pat, int n, int *_prep);
		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. */
		char kstrtok(const char str, const char sep, ks_tokaux_t aux);

		#ifdef __cplusplus
		}
		#endif

		static inline void ks_resize(kstring_t *s, size_t size)
		{
		if (s->m < size) {
		s->m = size;
		kroundup32(s->m);
		s->s = (char*)realloc(s->s, s->m);
		}
		}

		static inline int kputsn(const char p, int l, kstring_t s)
		{
		if (s->l + l + 1 >= s->m) {
		s->m = s->l + l + 2;
		kroundup32(s->m);
		s->s = (char*)realloc(s->s, s->m);
		}
		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 (s->l + 1 >= s->m) {
		s->m = s->l + 2;
		kroundup32(s->m);
		s->s = (char*)realloc(s->s, s->m);
		}
		s->s[s->l++] = c;
		s->s[s->l] = 0;
		return c;
		}

		static inline int kputw(int c, kstring_t *s)
		{
		char buf[16];
		int l, x;
		if (c == 0) return kputc('0', s);
		for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
		if (c < 0) buf[l++] = '-';
		if (s->l + l + 1 >= s->m) {
		s->m = s->l + l + 2;
		kroundup32(s->m);
		s->s = (char*)realloc(s->s, s->m);
		}
		for (x = l - 1; x >= 0; --x) s->s[s->l++] = buf[x];
		s->s[s->l] = 0;
		return 0;
		}

		static inline int kputuw(unsigned c, kstring_t *s)
		{
		char buf[16];
		int l, i;
		unsigned x;
		if (c == 0) return kputc('0', s);
		for (l = 0, x = c; x > 0; x /= 10) buf[l++] = x%10 + '0';
		if (s->l + l + 1 >= s->m) {
		s->m = s->l + l + 2;
		kroundup32(s->m);
		s->s = (char*)realloc(s->s, s->m);
		}
		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)
		{
		char buf[32];
		long l, x;
		if (c == 0) return kputc('0', s);
		for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
		if (c < 0) buf[l++] = '-';
		if (s->l + l + 1 >= s->m) {
		s->m = s->l + l + 2;
		kroundup32(s->m);
		s->s = (char*)realloc(s->s, s->m);
		}
		for (x = l - 1; x >= 0; --x) s->s[s->l++] = buf[x];
		s->s[s->l] = 0;
		return 0;
		}

		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

kvec.h

deleted100644 → 0

+0 −90

Original line number	Diff line number	Diff line
		/* The MIT License

		Copyright (c) 2008, by Attractive Chaos <attractor@live.co.uk>

		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.
		*/

		/*
		An example:

		#include "kvec.h"
		int main() {
		kvec_t(int) array;
		kv_init(array);
		kv_push(int, array, 10); // append
		kv_a(int, array, 20) = 5; // dynamic
		kv_A(array, 20) = 4; // static
		kv_destroy(array);
		return 0;
		}
		*/

		/*
		2008-09-22 (0.1.0):

		* The initial version.

		*/

		#ifndef AC_KVEC_H
		#define AC_KVEC_H

		#include <stdlib.h>

		#define kv_roundup32(x) (--(x), (x)\|=(x)>>1, (x)\|=(x)>>2, (x)\|=(x)>>4, (x)\|=(x)>>8, (x)\|=(x)>>16, ++(x))

		#define kvec_t(type) struct { size_t n, m; type *a; }
		#define kv_init(v) ((v).n = (v).m = 0, (v).a = 0)
		#define kv_destroy(v) free((v).a)
		#define kv_A(v, i) ((v).a[(i)])
		#define kv_pop(v) ((v).a[--(v).n])
		#define kv_size(v) ((v).n)
		#define kv_max(v) ((v).m)

		#define kv_resize(type, v, s) ((v).m = (s), (v).a = (type)realloc((v).a, sizeof(type) (v).m))

		#define kv_copy(type, v1, v0) do { \
		if ((v1).m < (v0).n) kv_resize(type, v1, (v0).n); \
		(v1).n = (v0).n; \
		memcpy((v1).a, (v0).a, sizeof(type) * (v0).n); \
		} while (0) \

		#define kv_push(type, v, x) do { \
		if ((v).n == (v).m) { \
		(v).m = (v).m? (v).m<<1 : 2; \
		(v).a = (type)realloc((v).a, sizeof(type) (v).m); \
		} \
		(v).a[(v).n++] = (x); \
		} while (0)

		#define kv_pushp(type, v) (((v).n == (v).m)? \
		((v).m = ((v).m? (v).m<<1 : 2), \
		(v).a = (type)realloc((v).a, sizeof(type) (v).m), 0) \
		: 0), ((v).a + ((v).n++))

		#define kv_a(type, v, i) (((v).m <= (size_t)(i)? \
		((v).m = (v).n = (i) + 1, kv_roundup32((v).m), \
		(v).a = (type)realloc((v).a, sizeof(type) (v).m), 0) \
		: (v).n <= (size_t)(i)? (v).n = (i) + 1 \
		: 0), (v).a[(i)])

		#endif