--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/kstring.c	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,254 @@
+/* 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;
+}
+
+/**********************
+ * 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