--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/samtools-0.1.16/faidx.c	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,423 @@
+#include <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include "faidx.h"
+#include "khash.h"
+
+typedef struct {
+	uint64_t len:32, line_len:16, line_blen:16;
+	uint64_t offset;
+} faidx1_t;
+KHASH_MAP_INIT_STR(s, faidx1_t)
+
+#ifndef _NO_RAZF
+#include "razf.h"
+#else
+#ifdef _WIN32
+#define ftello(fp) ftell(fp)
+#define fseeko(fp, offset, whence) fseek(fp, offset, whence)
+#else
+extern off_t ftello(FILE *stream);
+extern int fseeko(FILE *stream, off_t offset, int whence);
+#endif
+#define RAZF FILE
+#define razf_read(fp, buf, size) fread(buf, 1, size, fp)
+#define razf_open(fn, mode) fopen(fn, mode)
+#define razf_close(fp) fclose(fp)
+#define razf_seek(fp, offset, whence) fseeko(fp, offset, whence)
+#define razf_tell(fp) ftello(fp)
+#endif
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
+
+struct __faidx_t {
+	RAZF *rz;
+	int n, m;
+	char **name;
+	khash_t(s) *hash;
+};
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+static inline void fai_insert_index(faidx_t *idx, const char *name, int len, int line_len, int line_blen, uint64_t offset)
+{
+	khint_t k;
+	int ret;
+	faidx1_t t;
+	if (idx->n == idx->m) {
+		idx->m = idx->m? idx->m<<1 : 16;
+		idx->name = (char**)realloc(idx->name, sizeof(void*) * idx->m);
+	}
+	idx->name[idx->n] = strdup(name);
+	k = kh_put(s, idx->hash, idx->name[idx->n], &ret);
+	t.len = len; t.line_len = line_len; t.line_blen = line_blen; t.offset = offset;
+	kh_value(idx->hash, k) = t;
+	++idx->n;
+}
+
+faidx_t *fai_build_core(RAZF *rz)
+{
+	char c, *name;
+	int l_name, m_name, ret;
+	int len, line_len, line_blen, state;
+	int l1, l2;
+	faidx_t *idx;
+	uint64_t offset;
+
+	idx = (faidx_t*)calloc(1, sizeof(faidx_t));
+	idx->hash = kh_init(s);
+	name = 0; l_name = m_name = 0;
+	len = line_len = line_blen = -1; state = 0; l1 = l2 = -1; offset = 0;
+	while (razf_read(rz, &c, 1)) {
+		if (c == '\n') { // an empty line
+			if (state == 1) {
+				offset = razf_tell(rz);
+				continue;
+			} else if ((state == 0 && len < 0) || state == 2) continue;
+		}
+		if (c == '>') { // fasta header
+			if (len >= 0)
+				fai_insert_index(idx, name, len, line_len, line_blen, offset);
+			l_name = 0;
+			while ((ret = razf_read(rz, &c, 1)) != 0 && !isspace(c)) {
+				if (m_name < l_name + 2) {
+					m_name = l_name + 2;
+					kroundup32(m_name);
+					name = (char*)realloc(name, m_name);
+				}
+				name[l_name++] = c;
+			}
+			name[l_name] = '\0';
+			if (ret == 0) {
+				fprintf(stderr, "[fai_build_core] the last entry has no sequence\n");
+				free(name); fai_destroy(idx);
+				return 0;
+			}
+			if (c != '\n') while (razf_read(rz, &c, 1) && c != '\n');
+			state = 1; len = 0;
+			offset = razf_tell(rz);
+		} else {
+			if (state == 3) {
+				fprintf(stderr, "[fai_build_core] inlined empty line is not allowed in sequence '%s'.\n", name);
+				free(name); fai_destroy(idx);
+				return 0;
+			}
+			if (state == 2) state = 3;
+			l1 = l2 = 0;
+			do {
+				++l1;
+				if (isgraph(c)) ++l2;
+			} while ((ret = razf_read(rz, &c, 1)) && c != '\n');
+			if (state == 3 && l2) {
+				fprintf(stderr, "[fai_build_core] different line length in sequence '%s'.\n", name);
+				free(name); fai_destroy(idx);
+				return 0;
+			}
+			++l1; len += l2;
+			if (l2 >= 0x10000) {
+				fprintf(stderr, "[fai_build_core] line length exceeds 65535 in sequence '%s'.\n", name);
+				free(name); fai_destroy(idx);
+				return 0;
+			}
+			if (state == 1) line_len = l1, line_blen = l2, state = 0;
+			else if (state == 0) {
+				if (l1 != line_len || l2 != line_blen) state = 2;
+			}
+		}
+	}
+	fai_insert_index(idx, name, len, line_len, line_blen, offset);
+	free(name);
+	return idx;
+}
+
+void fai_save(const faidx_t *fai, FILE *fp)
+{
+	khint_t k;
+	int i;
+	for (i = 0; i < fai->n; ++i) {
+		faidx1_t x;
+		k = kh_get(s, fai->hash, fai->name[i]);
+		x = kh_value(fai->hash, k);
+#ifdef _WIN32
+		fprintf(fp, "%s\t%d\t%ld\t%d\t%d\n", fai->name[i], (int)x.len, (long)x.offset, (int)x.line_blen, (int)x.line_len);
+#else
+		fprintf(fp, "%s\t%d\t%lld\t%d\t%d\n", fai->name[i], (int)x.len, (long long)x.offset, (int)x.line_blen, (int)x.line_len);
+#endif
+	}
+}
+
+faidx_t *fai_read(FILE *fp)
+{
+	faidx_t *fai;
+	char *buf, *p;
+	int len, line_len, line_blen;
+#ifdef _WIN32
+	long offset;
+#else
+	long long offset;
+#endif
+	fai = (faidx_t*)calloc(1, sizeof(faidx_t));
+	fai->hash = kh_init(s);
+	buf = (char*)calloc(0x10000, 1);
+	while (!feof(fp) && fgets(buf, 0x10000, fp)) {
+		for (p = buf; *p && isgraph(*p); ++p);
+		*p = 0; ++p;
+#ifdef _WIN32
+		sscanf(p, "%d%ld%d%d", &len, &offset, &line_blen, &line_len);
+#else
+		sscanf(p, "%d%lld%d%d", &len, &offset, &line_blen, &line_len);
+#endif
+		fai_insert_index(fai, buf, len, line_len, line_blen, offset);
+	}
+	free(buf);
+	return fai;
+}
+
+void fai_destroy(faidx_t *fai)
+{
+	int i;
+	for (i = 0; i < fai->n; ++i) free(fai->name[i]);
+	free(fai->name);
+	kh_destroy(s, fai->hash);
+	if (fai->rz) razf_close(fai->rz);
+	free(fai);
+}
+
+int fai_build(const char *fn)
+{
+	char *str;
+	RAZF *rz;
+	FILE *fp;
+	faidx_t *fai;
+	str = (char*)calloc(strlen(fn) + 5, 1);
+	sprintf(str, "%s.fai", fn);
+	rz = razf_open(fn, "r");
+	if (rz == 0) {
+		fprintf(stderr, "[fai_build] fail to open the FASTA file %s\n",fn);
+		free(str);
+		return -1;
+	}
+	fai = fai_build_core(rz);
+	razf_close(rz);
+	fp = fopen(str, "wb");
+	if (fp == 0) {
+		fprintf(stderr, "[fai_build] fail to write FASTA index %s\n",str);
+		fai_destroy(fai); free(str);
+		return -1;
+	}
+	fai_save(fai, fp);
+	fclose(fp);
+	free(str);
+	fai_destroy(fai);
+	return 0;
+}
+
+#ifdef _USE_KNETFILE
+FILE *download_and_open(const char *fn)
+{
+    const int buf_size = 1 * 1024 * 1024;
+    uint8_t *buf;
+    FILE *fp;
+    knetFile *fp_remote;
+    const char *url = fn;
+    const char *p;
+    int l = strlen(fn);
+    for (p = fn + l - 1; p >= fn; --p)
+        if (*p == '/') break;
+    fn = p + 1;
+
+    // First try to open a local copy
+    fp = fopen(fn, "r");
+    if (fp)
+        return fp;
+
+    // If failed, download from remote and open
+    fp_remote = knet_open(url, "rb");
+    if (fp_remote == 0) {
+        fprintf(stderr, "[download_from_remote] fail to open remote file %s\n",url);
+        return NULL;
+    }
+    if ((fp = fopen(fn, "wb")) == 0) {
+        fprintf(stderr, "[download_from_remote] fail to create file in the working directory %s\n",fn);
+        knet_close(fp_remote);
+        return NULL;
+    }
+    buf = (uint8_t*)calloc(buf_size, 1);
+    while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
+        fwrite(buf, 1, l, fp);
+    free(buf);
+    fclose(fp);
+    knet_close(fp_remote);
+
+    return fopen(fn, "r");
+}
+#endif
+
+faidx_t *fai_load(const char *fn)
+{
+	char *str;
+	FILE *fp;
+	faidx_t *fai;
+	str = (char*)calloc(strlen(fn) + 5, 1);
+	sprintf(str, "%s.fai", fn);
+
+#ifdef _USE_KNETFILE
+    if (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)
+    {
+        fp = download_and_open(str);
+        if ( !fp )
+        {
+            fprintf(stderr, "[fai_load] failed to open remote FASTA index %s\n", str);
+            free(str);
+            return 0;
+        }
+    }
+    else
+#endif
+        fp = fopen(str, "rb");
+	if (fp == 0) {
+		fprintf(stderr, "[fai_load] build FASTA index.\n");
+		fai_build(fn);
+		fp = fopen(str, "rb");
+		if (fp == 0) {
+			fprintf(stderr, "[fai_load] fail to open FASTA index.\n");
+			free(str);
+			return 0;
+		}
+	}
+
+	fai = fai_read(fp);
+	fclose(fp);
+
+	fai->rz = razf_open(fn, "rb");
+	free(str);
+	if (fai->rz == 0) {
+		fprintf(stderr, "[fai_load] fail to open FASTA file.\n");
+		return 0;
+	}
+	return fai;
+}
+
+char *fai_fetch(const faidx_t *fai, const char *str, int *len)
+{
+	char *s, *p, c;
+	int i, l, k;
+	khiter_t iter;
+	faidx1_t val;
+	khash_t(s) *h;
+	int beg, end;
+
+	beg = end = -1;
+	h = fai->hash;
+	l = strlen(str);
+	p = s = (char*)malloc(l+1);
+	/* squeeze out "," */
+	for (i = k = 0; i != l; ++i)
+		if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i];
+	s[k] = 0;
+	for (i = 0; i != k; ++i) if (s[i] == ':') break;
+	s[i] = 0;
+	iter = kh_get(s, h, s); /* get the ref_id */
+	if (iter == kh_end(h)) {
+		*len = 0;
+		free(s); return 0;
+	}
+	val = kh_value(h, iter);
+	if (i == k) { /* dump the whole sequence */
+		beg = 0; end = val.len;
+	} else {
+		for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
+		beg = atoi(p);
+		if (i < k) {
+			p = s + i + 1;
+			end = atoi(p);
+		} else end = val.len;
+	}
+	if (beg > 0) --beg;
+	if (beg >= val.len) beg = val.len;
+	if (end >= val.len) end = val.len;
+	if (beg > end) beg = end;
+	free(s);
+
+	// now retrieve the sequence
+	l = 0;
+	s = (char*)malloc(end - beg + 2);
+	razf_seek(fai->rz, val.offset + beg / val.line_blen * val.line_len + beg % val.line_blen, SEEK_SET);
+	while (razf_read(fai->rz, &c, 1) == 1 && l < end - beg && !fai->rz->z_err)
+		if (isgraph(c)) s[l++] = c;
+	s[l] = '\0';
+	*len = l;
+	return s;
+}
+
+int faidx_main(int argc, char *argv[])
+{
+	if (argc == 1) {
+		fprintf(stderr, "Usage: faidx <in.fasta> [<reg> [...]]\n");
+		return 1;
+	} else {
+		if (argc == 2) fai_build(argv[1]);
+		else {
+			int i, j, k, l;
+			char *s;
+			faidx_t *fai;
+			fai = fai_load(argv[1]);
+			if (fai == 0) return 1;
+			for (i = 2; i != argc; ++i) {
+				printf(">%s\n", argv[i]);
+				s = fai_fetch(fai, argv[i], &l);
+				for (j = 0; j < l; j += 60) {
+					for (k = 0; k < 60 && k < l - j; ++k)
+						putchar(s[j + k]);
+					putchar('\n');
+				}
+				free(s);
+			}
+			fai_destroy(fai);
+		}
+	}
+	return 0;
+}
+
+int faidx_fetch_nseq(const faidx_t *fai) 
+{
+	return fai->n;
+}
+
+char *faidx_fetch_seq(const faidx_t *fai, char *c_name, int p_beg_i, int p_end_i, int *len)
+{
+	int l;
+	char c;
+    khiter_t iter;
+    faidx1_t val;
+	char *seq=NULL;
+
+    // Adjust position
+    iter = kh_get(s, fai->hash, c_name);
+    if(iter == kh_end(fai->hash)) return 0;
+    val = kh_value(fai->hash, iter);
+	if(p_end_i < p_beg_i) p_beg_i = p_end_i;
+    if(p_beg_i < 0) p_beg_i = 0;
+    else if(val.len <= p_beg_i) p_beg_i = val.len - 1;
+    if(p_end_i < 0) p_end_i = 0;
+    else if(val.len <= p_end_i) p_end_i = val.len - 1;
+
+    // Now retrieve the sequence 
+	l = 0;
+	seq = (char*)malloc(p_end_i - p_beg_i + 2);
+	razf_seek(fai->rz, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);
+	while (razf_read(fai->rz, &c, 1) == 1 && l < p_end_i - p_beg_i + 1)
+		if (isgraph(c)) seq[l++] = c;
+	seq[l] = '\0';
+	*len = l;
+	return seq;
+}
+
+#ifdef FAIDX_MAIN
+int main(int argc, char *argv[]) { return faidx_main(argc, argv); }
+#endif