7df6e18265341f87a69fba808aa1f92f8ebca841
markd
  Wed Apr 15 13:39:42 2026 -0700
move copy of htslib

diff --git src/htslib/kstring.c src/htslib/kstring.c
deleted file mode 100644
index b84ee2c1203..00000000000
--- src/htslib/kstring.c
+++ /dev/null
@@ -1,274 +0,0 @@
-/* The MIT License
-
-   Copyright (C) 2011 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.
-*/
-
-#include <stdarg.h>
-#include <stdio.h>
-#include <ctype.h>
-#include <string.h>
-#include <stdint.h>
-#include "htslib/kstring.h"
-
-int kvsprintf(kstring_t *s, const char *fmt, va_list ap)
-{
-	va_list args;
-	int l;
-	va_copy(args, ap);
-	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) {
-		s->m = s->l + l + 2;
-		kroundup32(s->m);
-		s->s = (char*)realloc(s->s, s->m);
-		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, ks_tokaux_t *aux)
-{
-	const char *p, *start;
-	if (sep) { // set up the table
-		if (str == 0 && (aux->tab[0]&1)) return 0; // no need to set up if we have finished
-		aux->finished = 0;
-		if (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) aux->p = str - 1, aux->finished = 0;
-	if (aux->sep < 0) {
-		for (p = start = aux->p + 1; *p; ++p)
-			if (aux->tab[*p>>6]>>(*p&0x3f)&1) break;
-	} else {
-		for (p = start = aux->p + 1; *p; ++p)
-			if (*p == aux->sep) break;
-	}
-	aux->p = 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 = (int*)realloc(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(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 = 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) ks_resize(s, s->m + 200);
-		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;
-}
-
-/**********************
- * Boyer-Moore search *
- **********************/
-
-typedef unsigned char ubyte_t;
-
-// 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;
-	prep = (int*)calloc(m + 256, sizeof(int));
-	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));
-	{ // 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;
-}
-
-void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep)
-{
-	int i, j, *prep = 0, *bmGs, *bmBc;
-	const ubyte_t *str, *pat;
-	str = (const ubyte_t*)_str; pat = (const ubyte_t*)_pat;
-	prep = (_prep == 0 || *_prep == 0)? ksBM_prep(pat, m) : *_prep;
-	if (_prep && *_prep == 0) *_prep = prep;
-	bmGs = prep; bmBc = prep + m;
-	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 return (void*)(str + j);
-	}
-	if (_prep == 0) free(prep);
-	return 0;
-}
-
-char *kstrstr(const char *str, const char *pat, int **_prep)
-{
-	return (char*)kmemmem(str, strlen(str), pat, strlen(pat), _prep);
-}
-
-char *kstrnstr(const char *str, const char *pat, int n, int **_prep)
-{
-	return (char*)kmemmem(str, n, pat, strlen(pat), _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