--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/bwa-0.5.7-mh/bwt_gen/bwt_gen.h	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,105 @@
+/*
+
+   BWTConstruct.h		BWT-Index Construction
+
+   This module constructs BWT and auxiliary data structures.
+
+   Copyright (C) 2004, Wong Chi Kwong.
+
+   This program is free software; you can redistribute it and/or
+   modify it under the terms of the GNU General Public License
+   as published by the Free Software Foundation; either version 2
+   of the License, or (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program; if not, write to the Free Software
+   Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+
+*/
+
+#ifndef BWT_GEN_H
+#define BWT_GEN_H
+
+#define ALPHABET_SIZE				4
+#define BIT_PER_CHAR				2
+#define CHAR_PER_WORD				16
+#define CHAR_PER_BYTE				4
+
+#define BITS_IN_WORD 32
+#define BITS_IN_BYTE 8
+#define BYTES_IN_WORD 4
+
+#define ALL_ONE_MASK 0xFFFFFFFF
+#define DNA_OCC_CNT_TABLE_SIZE_IN_WORD	65536
+
+#define BITS_PER_OCC_VALUE			16
+#define OCC_VALUE_PER_WORD			2
+#define OCC_INTERVAL				256
+#define OCC_INTERVAL_MAJOR			65536
+
+#define TRUE    1
+#define FALSE   0
+
+#define BWTINC_INSERT_SORT_NUM_ITEM 7
+
+#define average(value1, value2)					( ((value1) & (value2)) + ((value1) ^ (value2)) / 2 )
+#define min(value1, value2)						( ((value1) < (value2)) ? (value1) : (value2) )
+#define max(value1, value2)						( ((value1) > (value2)) ? (value1) : (value2) )
+#define med3(a, b, c)							( a<b ? (b<c ? b : a<c ? c : a) : (b>c ? b : a>c ? c : a))
+#define swap(a, b, t);							t = a; a = b; b = t;
+#define truncateLeft(value, offset)				( (value) << (offset) >> (offset) )
+#define truncateRight(value, offset)			( (value) >> (offset) << (offset) )
+#define DNA_OCC_SUM_EXCEPTION(sum)			((sum & 0xfefefeff) == 0)
+
+typedef struct SaIndexRange {
+	unsigned int startSaIndex;
+	unsigned int endSaIndex;
+} SaIndexRange;
+
+typedef struct BWT {
+	unsigned int textLength;			// length of the text
+	unsigned int saInterval;			// interval between two SA values stored explicitly
+	unsigned int inverseSaInterval;		// interval between two inverse SA stored explicitly
+	unsigned int inverseSa0;			// SA-1[0]
+	unsigned int *cumulativeFreq;		// cumulative frequency
+	unsigned int *bwtCode;				// BWT code
+	unsigned int *occValue;				// Occurrence values stored explicitly
+	unsigned int *occValueMajor;		// Occurrence values stored explicitly
+	unsigned int *saValue;				// SA values stored explicitly
+	unsigned int *inverseSa;			// Inverse SA stored explicitly
+	SaIndexRange *saIndexRange;			// SA index range
+	int saIndexRangeNumOfChar;			// Number of characters indexed in SA index range
+	unsigned int *saValueOnBoundary;	// Pre-calculated frequently referred data
+	unsigned int *decodeTable;			// For decoding BWT by table lookup
+	unsigned int decodeTableGenerated;	// == TRUE if decode table is generated on load and will be freed
+	unsigned int bwtSizeInWord;			// Temporary variable to hold the memory allocated
+	unsigned int occSizeInWord;			// Temporary variable to hold the memory allocated
+	unsigned int occMajorSizeInWord;	// Temporary variable to hold the memory allocated
+	unsigned int saValueSize;			// Temporary variable to hold the memory allocated
+	unsigned int inverseSaSize;			// Temporary variable to hold the memory allocated
+	unsigned int saIndexRangeSize;		// Temporary variable to hold the memory allocated
+} BWT;
+
+typedef struct BWTInc {
+	BWT *bwt;
+	unsigned int numberOfIterationDone;
+	unsigned int *cumulativeCountInCurrentBuild;
+	unsigned int availableWord;
+	unsigned int targetTextLength;
+	float targetNBit;
+	unsigned int buildSize;
+	unsigned int initialMaxBuildSize;
+	unsigned int incMaxBuildSize;
+	unsigned int firstCharInLastIteration;
+	unsigned int *workingMemory;
+	unsigned int *packedText;
+	unsigned char *textBuffer;
+	unsigned int *packedShift;
+} BWTInc;
+
+#endif