X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=tabix%2Fkstring.c;fp=tabix%2Fkstring.c;h=0000000000000000000000000000000000000000;hp=e0203fa3e877604f53291b39ff6a2f273e6dff8f;hb=d02fe5283ed7a93a2f76a5d6dc6e37b40c11b9b1;hpb=d828f9c9aa78e3d1687265b52de841f3f3852089

diff --git a/tabix/kstring.c b/tabix/kstring.c
deleted file mode 100644
index e0203fa..0000000
--- a/tabix/kstring.c
+++ /dev/null
@@ -1,165 +0,0 @@
-#include <stdarg.h>
-#include <stdio.h>
-#include <ctype.h>
-#include <string.h>
-#include <stdint.h>
-#include "kstring.h"
-
-int ksprintf(kstring_t *s, const char *fmt, ...)
-{
-	va_list ap;
-	int l;
-	va_start(ap, fmt);
-	l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap); // This line does not work with glibc 2.0. See `man snprintf'.
-	va_end(ap);
-	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_start(ap, fmt);
-		l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap);
-	}
-	va_end(ap);
-	s->l += l;
-	return l;
-}
-
-// 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) {												\
-				max = max? max<<1 : 2;									\
-				offsets = (int*)realloc(offsets, sizeof(int) * max);	\
-			}															\
-			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 *
- **********************/
-
-// reference: http://www-igm.univ-mlv.fr/~lecroq/string/node14.html
-int *ksBM_prep(const uint8_t *pat, int m)
-{
-	int i, *suff, *prep, *bmGs, *bmBc;
-	prep = calloc(m + 256, 1);
-	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 = 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;
-}
-
-int *ksBM_search(const uint8_t *str, int n, const uint8_t *pat, int m, int *_prep, int *n_matches)
-{
-	int i, j, *prep, *bmGs, *bmBc;
-	int *matches = 0, mm = 0, nm = 0;
-	prep = _prep? _prep : ksBM_prep(pat, m);
-	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) {
-			if (nm == mm) {
-				mm = mm? mm<<1 : 1;
-				matches = realloc(matches, mm * sizeof(int));
-			}
-			matches[nm++] = j;
-			j += bmGs[0];
-		} else {
-			int max = bmBc[str[i+j]] - m + 1 + i;
-			if (max < bmGs[i]) max = bmGs[i];
-			j += max;
-		}
-	}
-	*n_matches = nm;
-	if (_prep == 0) free(prep);
-	return matches;
-}
-
-#ifdef KSTRING_MAIN
-#include <stdio.h>
-int main()
-{
-	kstring_t *s;
-	int *fields, n, i;
-	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]);
-	free(s);
-
-	{
-		static char *str = "abcdefgcdg";
-		static char *pat = "cd";
-		int n, *matches;
-		matches = ksBM_search(str, strlen(str), pat, strlen(pat), 0, &n);
-		printf("%d: \n", n);
-		for (i = 0; i < n; ++i)
-			printf("- %d\n", matches[i]);
-		free(matches);
-	}
-	return 0;
-}
-#endif