--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/bwa-0.5.7-mh/khash.h	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,506 @@
+/* The MIT License
+
+   Copyright (c) 2008, 2009 by attractor <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 "khash.h"
+KHASH_MAP_INIT_INT(32, char)
+int main() {
+	int ret, is_missing;
+	khiter_t k;
+	khash_t(32) *h = kh_init(32);
+	k = kh_put(32, h, 5, &ret);
+	if (!ret) kh_del(32, h, k);
+	kh_value(h, k) = 10;
+	k = kh_get(32, h, 10);
+	is_missing = (k == kh_end(h));
+	k = kh_get(32, h, 5);
+	kh_del(32, h, k);
+	for (k = kh_begin(h); k != kh_end(h); ++k)
+		if (kh_exist(h, k)) kh_value(h, k) = 1;
+	kh_destroy(32, h);
+	return 0;
+}
+*/
+
+/*
+  2009-09-26 (0.2.4):
+
+    * Improve portability
+
+  2008-09-19 (0.2.3):
+
+	* Corrected the example
+	* Improved interfaces
+
+  2008-09-11 (0.2.2):
+
+	* Improved speed a little in kh_put()
+
+  2008-09-10 (0.2.1):
+
+	* Added kh_clear()
+	* Fixed a compiling error
+
+  2008-09-02 (0.2.0):
+
+	* Changed to token concatenation which increases flexibility.
+
+  2008-08-31 (0.1.2):
+
+	* Fixed a bug in kh_get(), which has not been tested previously.
+
+  2008-08-31 (0.1.1):
+
+	* Added destructor
+*/
+
+
+#ifndef __AC_KHASH_H
+#define __AC_KHASH_H
+
+/*!
+  @header
+
+  Generic hash table library.
+
+  @copyright Heng Li
+ */
+
+#define AC_VERSION_KHASH_H "0.2.4"
+
+#include <stdlib.h>
+#include <string.h>
+#include <limits.h>
+
+/* compipler specific configuration */
+
+#if UINT_MAX == 0xffffffffu
+typedef unsigned int khint32_t;
+#elif ULONG_MAX == 0xffffffffu
+typedef unsigned long khint32_t;
+#endif
+
+#if ULONG_MAX == ULLONG_MAX
+typedef unsigned long khint64_t;
+#else
+typedef unsigned long long khint64_t;
+#endif
+
+#ifdef _MSC_VER
+#define inline __inline
+#endif
+
+typedef khint32_t khint_t;
+typedef khint_t khiter_t;
+
+#define __ac_HASH_PRIME_SIZE 32
+static const khint32_t __ac_prime_list[__ac_HASH_PRIME_SIZE] =
+{
+  0ul,          3ul,          11ul,         23ul,         53ul,
+  97ul,         193ul,        389ul,        769ul,        1543ul,
+  3079ul,       6151ul,       12289ul,      24593ul,      49157ul,
+  98317ul,      196613ul,     393241ul,     786433ul,     1572869ul,
+  3145739ul,    6291469ul,    12582917ul,   25165843ul,   50331653ul,
+  100663319ul,  201326611ul,  402653189ul,  805306457ul,  1610612741ul,
+  3221225473ul, 4294967291ul
+};
+
+#define __ac_isempty(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&2)
+#define __ac_isdel(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&1)
+#define __ac_iseither(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&3)
+#define __ac_set_isdel_false(flag, i) (flag[i>>4]&=~(1ul<<((i&0xfU)<<1)))
+#define __ac_set_isempty_false(flag, i) (flag[i>>4]&=~(2ul<<((i&0xfU)<<1)))
+#define __ac_set_isboth_false(flag, i) (flag[i>>4]&=~(3ul<<((i&0xfU)<<1)))
+#define __ac_set_isdel_true(flag, i) (flag[i>>4]|=1ul<<((i&0xfU)<<1))
+
+static const double __ac_HASH_UPPER = 0.77;
+
+#define KHASH_INIT(name, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
+	typedef struct {													\
+		khint_t n_buckets, size, n_occupied, upper_bound;				\
+		khint32_t *flags;												\
+		khkey_t *keys;													\
+		khval_t *vals;													\
+	} kh_##name##_t;													\
+	static inline kh_##name##_t *kh_init_##name() {						\
+		return (kh_##name##_t*)calloc(1, sizeof(kh_##name##_t));		\
+	}																	\
+	static inline void kh_destroy_##name(kh_##name##_t *h)				\
+	{																	\
+		if (h) {														\
+			free(h->keys); free(h->flags);								\
+			free(h->vals);												\
+			free(h);													\
+		}																\
+	}																	\
+	static inline void kh_clear_##name(kh_##name##_t *h)				\
+	{																	\
+		if (h && h->flags) {											\
+			memset(h->flags, 0xaa, ((h->n_buckets>>4) + 1) * sizeof(khint32_t)); \
+			h->size = h->n_occupied = 0;								\
+		}																\
+	}																	\
+	static inline khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \
+	{																	\
+		if (h->n_buckets) {												\
+			khint_t inc, k, i, last;									\
+			k = __hash_func(key); i = k % h->n_buckets;					\
+			inc = 1 + k % (h->n_buckets - 1); last = i;					\
+			while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \
+				if (i + inc >= h->n_buckets) i = i + inc - h->n_buckets; \
+				else i += inc;											\
+				if (i == last) return h->n_buckets;						\
+			}															\
+			return __ac_iseither(h->flags, i)? h->n_buckets : i;		\
+		} else return 0;												\
+	}																	\
+	static inline void kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets) \
+	{																	\
+		khint32_t *new_flags = 0;										\
+		khint_t j = 1;													\
+		{																\
+			khint_t t = __ac_HASH_PRIME_SIZE - 1;						\
+			while (__ac_prime_list[t] > new_n_buckets) --t;				\
+			new_n_buckets = __ac_prime_list[t+1];						\
+			if (h->size >= (khint_t)(new_n_buckets * __ac_HASH_UPPER + 0.5)) j = 0;	\
+			else {														\
+				new_flags = (khint32_t*)malloc(((new_n_buckets>>4) + 1) * sizeof(khint32_t));	\
+				memset(new_flags, 0xaa, ((new_n_buckets>>4) + 1) * sizeof(khint32_t)); \
+				if (h->n_buckets < new_n_buckets) {						\
+					h->keys = (khkey_t*)realloc(h->keys, new_n_buckets * sizeof(khkey_t)); \
+					if (kh_is_map)										\
+						h->vals = (khval_t*)realloc(h->vals, new_n_buckets * sizeof(khval_t)); \
+				}														\
+			}															\
+		}																\
+		if (j) {														\
+			for (j = 0; j != h->n_buckets; ++j) {						\
+				if (__ac_iseither(h->flags, j) == 0) {					\
+					khkey_t key = h->keys[j];							\
+					khval_t val;										\
+					if (kh_is_map) val = h->vals[j];					\
+					__ac_set_isdel_true(h->flags, j);					\
+					while (1) {											\
+						khint_t inc, k, i;								\
+						k = __hash_func(key);							\
+						i = k % new_n_buckets;							\
+						inc = 1 + k % (new_n_buckets - 1);				\
+						while (!__ac_isempty(new_flags, i)) {			\
+							if (i + inc >= new_n_buckets) i = i + inc - new_n_buckets; \
+							else i += inc;								\
+						}												\
+						__ac_set_isempty_false(new_flags, i);			\
+						if (i < h->n_buckets && __ac_iseither(h->flags, i) == 0) { \
+							{ khkey_t tmp = h->keys[i]; h->keys[i] = key; key = tmp; } \
+							if (kh_is_map) { khval_t tmp = h->vals[i]; h->vals[i] = val; val = tmp; } \
+							__ac_set_isdel_true(h->flags, i);			\
+						} else {										\
+							h->keys[i] = key;							\
+							if (kh_is_map) h->vals[i] = val;			\
+							break;										\
+						}												\
+					}													\
+				}														\
+			}															\
+			if (h->n_buckets > new_n_buckets) {							\
+				h->keys = (khkey_t*)realloc(h->keys, new_n_buckets * sizeof(khkey_t)); \
+				if (kh_is_map)											\
+					h->vals = (khval_t*)realloc(h->vals, new_n_buckets * sizeof(khval_t)); \
+			}															\
+			free(h->flags);												\
+			h->flags = new_flags;										\
+			h->n_buckets = new_n_buckets;								\
+			h->n_occupied = h->size;									\
+			h->upper_bound = (khint_t)(h->n_buckets * __ac_HASH_UPPER + 0.5); \
+		}																\
+	}																	\
+	static inline khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
+	{																	\
+		khint_t x;														\
+		if (h->n_occupied >= h->upper_bound) {							\
+			if (h->n_buckets > (h->size<<1)) kh_resize_##name(h, h->n_buckets - 1); \
+			else kh_resize_##name(h, h->n_buckets + 1);					\
+		}																\
+		{																\
+			khint_t inc, k, i, site, last;								\
+			x = site = h->n_buckets; k = __hash_func(key); i = k % h->n_buckets; \
+			if (__ac_isempty(h->flags, i)) x = i;						\
+			else {														\
+				inc = 1 + k % (h->n_buckets - 1); last = i;				\
+				while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \
+					if (__ac_isdel(h->flags, i)) site = i;				\
+					if (i + inc >= h->n_buckets) i = i + inc - h->n_buckets; \
+					else i += inc;										\
+					if (i == last) { x = site; break; }					\
+				}														\
+				if (x == h->n_buckets) {								\
+					if (__ac_isempty(h->flags, i) && site != h->n_buckets) x = site; \
+					else x = i;											\
+				}														\
+			}															\
+		}																\
+		if (__ac_isempty(h->flags, x)) {								\
+			h->keys[x] = key;											\
+			__ac_set_isboth_false(h->flags, x);							\
+			++h->size; ++h->n_occupied;									\
+			*ret = 1;													\
+		} else if (__ac_isdel(h->flags, x)) {							\
+			h->keys[x] = key;											\
+			__ac_set_isboth_false(h->flags, x);							\
+			++h->size;													\
+			*ret = 2;													\
+		} else *ret = 0;												\
+		return x;														\
+	}																	\
+	static inline void kh_del_##name(kh_##name##_t *h, khint_t x)		\
+	{																	\
+		if (x != h->n_buckets && !__ac_iseither(h->flags, x)) {			\
+			__ac_set_isdel_true(h->flags, x);							\
+			--h->size;													\
+		}																\
+	}
+
+/* --- BEGIN OF HASH FUNCTIONS --- */
+
+/*! @function
+  @abstract     Integer hash function
+  @param  key   The integer [khint32_t]
+  @return       The hash value [khint_t]
+ */
+#define kh_int_hash_func(key) (khint32_t)(key)
+/*! @function
+  @abstract     Integer comparison function
+ */
+#define kh_int_hash_equal(a, b) ((a) == (b))
+/*! @function
+  @abstract     64-bit integer hash function
+  @param  key   The integer [khint64_t]
+  @return       The hash value [khint_t]
+ */
+#define kh_int64_hash_func(key) (khint32_t)((key)>>33^(key)^(key)<<11)
+/*! @function
+  @abstract     64-bit integer comparison function
+ */
+#define kh_int64_hash_equal(a, b) ((a) == (b))
+/*! @function
+  @abstract     const char* hash function
+  @param  s     Pointer to a null terminated string
+  @return       The hash value
+ */
+static inline khint_t __ac_X31_hash_string(const char *s)
+{
+	khint_t h = *s;
+	if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
+	return h;
+}
+/*! @function
+  @abstract     Another interface to const char* hash function
+  @param  key   Pointer to a null terminated string [const char*]
+  @return       The hash value [khint_t]
+ */
+#define kh_str_hash_func(key) __ac_X31_hash_string(key)
+/*! @function
+  @abstract     Const char* comparison function
+ */
+#define kh_str_hash_equal(a, b) (strcmp(a, b) == 0)
+
+/* --- END OF HASH FUNCTIONS --- */
+
+/* Other necessary macros... */
+
+/*!
+  @abstract Type of the hash table.
+  @param  name  Name of the hash table [symbol]
+ */
+#define khash_t(name) kh_##name##_t
+
+/*! @function
+  @abstract     Initiate a hash table.
+  @param  name  Name of the hash table [symbol]
+  @return       Pointer to the hash table [khash_t(name)*]
+ */
+#define kh_init(name) kh_init_##name()
+
+/*! @function
+  @abstract     Destroy a hash table.
+  @param  name  Name of the hash table [symbol]
+  @param  h     Pointer to the hash table [khash_t(name)*]
+ */
+#define kh_destroy(name, h) kh_destroy_##name(h)
+
+/*! @function
+  @abstract     Reset a hash table without deallocating memory.
+  @param  name  Name of the hash table [symbol]
+  @param  h     Pointer to the hash table [khash_t(name)*]
+ */
+#define kh_clear(name, h) kh_clear_##name(h)
+
+/*! @function
+  @abstract     Resize a hash table.
+  @param  name  Name of the hash table [symbol]
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  s     New size [khint_t]
+ */
+#define kh_resize(name, h, s) kh_resize_##name(h, s)
+
+/*! @function
+  @abstract     Insert a key to the hash table.
+  @param  name  Name of the hash table [symbol]
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  k     Key [type of keys]
+  @param  r     Extra return code: 0 if the key is present in the hash table;
+                1 if the bucket is empty (never used); 2 if the element in
+				the bucket has been deleted [int*]
+  @return       Iterator to the inserted element [khint_t]
+ */
+#define kh_put(name, h, k, r) kh_put_##name(h, k, r)
+
+/*! @function
+  @abstract     Retrieve a key from the hash table.
+  @param  name  Name of the hash table [symbol]
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  k     Key [type of keys]
+  @return       Iterator to the found element, or kh_end(h) is the element is absent [khint_t]
+ */
+#define kh_get(name, h, k) kh_get_##name(h, k)
+
+/*! @function
+  @abstract     Remove a key from the hash table.
+  @param  name  Name of the hash table [symbol]
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  k     Iterator to the element to be deleted [khint_t]
+ */
+#define kh_del(name, h, k) kh_del_##name(h, k)
+
+
+/*! @function
+  @abstract     Test whether a bucket contains data.
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  x     Iterator to the bucket [khint_t]
+  @return       1 if containing data; 0 otherwise [int]
+ */
+#define kh_exist(h, x) (!__ac_iseither((h)->flags, (x)))
+
+/*! @function
+  @abstract     Get key given an iterator
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  x     Iterator to the bucket [khint_t]
+  @return       Key [type of keys]
+ */
+#define kh_key(h, x) ((h)->keys[x])
+
+/*! @function
+  @abstract     Get value given an iterator
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  x     Iterator to the bucket [khint_t]
+  @return       Value [type of values]
+  @discussion   For hash sets, calling this results in segfault.
+ */
+#define kh_val(h, x) ((h)->vals[x])
+
+/*! @function
+  @abstract     Alias of kh_val()
+ */
+#define kh_value(h, x) ((h)->vals[x])
+
+/*! @function
+  @abstract     Get the start iterator
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @return       The start iterator [khint_t]
+ */
+#define kh_begin(h) (khint_t)(0)
+
+/*! @function
+  @abstract     Get the end iterator
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @return       The end iterator [khint_t]
+ */
+#define kh_end(h) ((h)->n_buckets)
+
+/*! @function
+  @abstract     Get the number of elements in the hash table
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @return       Number of elements in the hash table [khint_t]
+ */
+#define kh_size(h) ((h)->size)
+
+/*! @function
+  @abstract     Get the number of buckets in the hash table
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @return       Number of buckets in the hash table [khint_t]
+ */
+#define kh_n_buckets(h) ((h)->n_buckets)
+
+/* More conenient interfaces */
+
+/*! @function
+  @abstract     Instantiate a hash set containing integer keys
+  @param  name  Name of the hash table [symbol]
+ */
+#define KHASH_SET_INIT_INT(name)										\
+	KHASH_INIT(name, khint32_t, char, 0, kh_int_hash_func, kh_int_hash_equal)
+
+/*! @function
+  @abstract     Instantiate a hash map containing integer keys
+  @param  name  Name of the hash table [symbol]
+  @param  khval_t  Type of values [type]
+ */
+#define KHASH_MAP_INIT_INT(name, khval_t)								\
+	KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
+
+/*! @function
+  @abstract     Instantiate a hash map containing 64-bit integer keys
+  @param  name  Name of the hash table [symbol]
+ */
+#define KHASH_SET_INIT_INT64(name)										\
+	KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal)
+
+/*! @function
+  @abstract     Instantiate a hash map containing 64-bit integer keys
+  @param  name  Name of the hash table [symbol]
+  @param  khval_t  Type of values [type]
+ */
+#define KHASH_MAP_INIT_INT64(name, khval_t)								\
+	KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
+
+typedef const char *kh_cstr_t;
+/*! @function
+  @abstract     Instantiate a hash map containing const char* keys
+  @param  name  Name of the hash table [symbol]
+ */
+#define KHASH_SET_INIT_STR(name)										\
+	KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)
+
+/*! @function
+  @abstract     Instantiate a hash map containing const char* keys
+  @param  name  Name of the hash table [symbol]
+  @param  khval_t  Type of values [type]
+ */
+#define KHASH_MAP_INIT_STR(name, khval_t)								\
+	KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
+
+#endif /* __AC_KHASH_H */