bio-bwa 0.2.0

data/ext/bwt_gen/QSufSort.h

@@ -0,0 +1,40 @@
+/* QSufSort.h
+
+   Header file for QSufSort.c
+
+   This file contains an implementation of the algorithm presented in "Faster
+   Suffix Sorting" by N. Jesper Larsson (jesper@cs.lth.se) and Kunihiko
+   Sadakane (sada@is.s.u-tokyo.ac.jp).
+
+   This software may be used freely for any purpose. However, when distributed,
+   the original source must be clearly stated, and, when the source code is
+   distributed, the copyright notice must be retained and any alterations in
+   the code must be clearly marked. No warranty is given regarding the quality
+   of this software.
+
+   Modified by Wong Chi-Kwong, 2004
+
+   Changes summary:	- Used long variable and function names
+					- Removed global variables
+					- Replace pointer references with array references
+					- Used insertion sort in place of selection sort and increased insertion sort threshold
+					- Reconstructing suffix array from inverse becomes an option
+					- Add handling where end-of-text symbol is not necessary < all characters
+					- Removed codes for supporting alphabet size > number of characters
+  
+  No warrenty is given regarding the quality of the modifications.
+
+*/
+
+#ifndef __QSUFSORT_H__
+#define __QSUFSORT_H__
+
+#define KEY(V, I, p, h)					( V[ I[p] + h ] )
+#define INSERT_SORT_NUM_ITEM	16
+
+void QSufSortSuffixSort(int* __restrict V, int* __restrict I, const int numChar, const int largestInputSymbol, 
+						const int smallestInputSymbol, const int skipTransform);
+void QSufSortGenerateSaFromInverse(const int *V, int* __restrict I, const int numChar);
+
+
+#endif

data/ext/bwt_gen/bwt_gen.c

@@ -0,0 +1,1547 @@
+/*
+
+   BWTConstruct.c		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.
+
+*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "bwt_gen.h"
+#include "QSufSort.h"
+
+static unsigned int TextLengthFromBytePacked(unsigned int bytePackedLength, unsigned int bitPerChar,
+											 unsigned int lastByteLength)
+{
+	if (bytePackedLength > ALL_ONE_MASK / (BITS_IN_BYTE / bitPerChar)) {
+		fprintf(stderr, "TextLengthFromBytePacked(): text length > 2^32!\n");
+		exit(1);
+	}
+	return (bytePackedLength - 1) * (BITS_IN_BYTE / bitPerChar) + lastByteLength;
+}
+
+static void initializeVAL(unsigned int *startAddr, const unsigned int length, const unsigned int initValue)
+{
+	unsigned int i;
+	for (i=0; i<length; i++) startAddr[i] = initValue;
+}
+
+static void GenerateDNAOccCountTable(unsigned int *dnaDecodeTable)
+{
+	unsigned int i, j, c, t;
+
+	for (i=0; i<DNA_OCC_CNT_TABLE_SIZE_IN_WORD; i++) {
+		dnaDecodeTable[i] = 0;
+		c = i;
+		for (j=0; j<8; j++) {
+			t = c & 0x00000003;
+			dnaDecodeTable[i] += 1 << (t * 8);
+			c >>= 2;
+		}
+	}
+
+}
+// for BWTIncCreate()
+static unsigned int BWTOccValueMajorSizeInWord(const unsigned int numChar)
+{
+	unsigned int numOfOccValue;
+	unsigned int numOfOccIntervalPerMajor;
+	numOfOccValue = (numChar + OCC_INTERVAL - 1) / OCC_INTERVAL + 1; // Value at both end for bi-directional encoding
+	numOfOccIntervalPerMajor = OCC_INTERVAL_MAJOR / OCC_INTERVAL;
+	return (numOfOccValue + numOfOccIntervalPerMajor - 1) / numOfOccIntervalPerMajor * ALPHABET_SIZE;
+}
+// for BWTIncCreate()
+static unsigned int BWTOccValueMinorSizeInWord(const unsigned int numChar)
+{
+	unsigned int numOfOccValue;
+	numOfOccValue = (numChar + OCC_INTERVAL - 1) / OCC_INTERVAL + 1;		// Value at both end for bi-directional encoding
+	return (numOfOccValue + OCC_VALUE_PER_WORD - 1) / OCC_VALUE_PER_WORD * ALPHABET_SIZE;
+}
+// for BWTIncCreate()
+static unsigned int BWTResidentSizeInWord(const unsigned int numChar) {
+
+	unsigned int numCharRoundUpToOccInterval;
+
+	// The $ in BWT at the position of inverseSa0 is not encoded
+	numCharRoundUpToOccInterval = (numChar + OCC_INTERVAL - 1) / OCC_INTERVAL * OCC_INTERVAL;
+
+	return (numCharRoundUpToOccInterval + CHAR_PER_WORD - 1) / CHAR_PER_WORD;
+
+}
+
+static void BWTIncSetBuildSizeAndTextAddr(BWTInc *bwtInc)
+{
+	unsigned int maxBuildSize;
+
+	if (bwtInc->bwt->textLength == 0) {
+		// initial build
+		// Minus 2 because n+1 entries of seq and rank needed for n char
+		maxBuildSize = (bwtInc->availableWord - 2 - OCC_INTERVAL / CHAR_PER_WORD)
+							/ (2 * CHAR_PER_WORD + 1) * CHAR_PER_WORD;
+		if (bwtInc->initialMaxBuildSize > 0) {
+			bwtInc->buildSize = min(bwtInc->initialMaxBuildSize, maxBuildSize);
+		} else {
+			bwtInc->buildSize = maxBuildSize;
+		}
+	} else {
+		// Minus 3 because n+1 entries of sorted rank, seq and rank needed for n char
+		// Minus numberOfIterationDone because bwt slightly shift to left in each iteration
+		maxBuildSize = (bwtInc->availableWord - bwtInc->bwt->bwtSizeInWord - bwtInc->bwt->occSizeInWord - 3
+							 - bwtInc->numberOfIterationDone * OCC_INTERVAL / BIT_PER_CHAR) 
+							 / 3;
+		if (maxBuildSize < CHAR_PER_WORD) {
+			fprintf(stderr, "BWTIncSetBuildSizeAndTextAddr(): Not enough space allocated to continue construction!\n");
+			exit(1);
+		}
+		if (bwtInc->incMaxBuildSize > 0) {
+            bwtInc->buildSize = min(bwtInc->incMaxBuildSize, maxBuildSize);
+		} else {
+			bwtInc->buildSize = maxBuildSize;
+		}
+		if (bwtInc->buildSize < CHAR_PER_WORD) {
+			bwtInc->buildSize = CHAR_PER_WORD;
+		}
+	}
+
+	if (bwtInc->buildSize < CHAR_PER_WORD) {
+		fprintf(stderr, "BWTIncSetBuildSizeAndTextAddr(): Not enough space allocated to continue construction!\n");
+		exit(1);
+	}
+
+	bwtInc->buildSize = bwtInc->buildSize / CHAR_PER_WORD * CHAR_PER_WORD;
+
+	bwtInc->packedText = bwtInc->workingMemory + 2 * (bwtInc->buildSize + 1);
+	bwtInc->textBuffer = (unsigned char*)(bwtInc->workingMemory + bwtInc->buildSize + 1);
+
+}
+
+// for ceilLog2()
+unsigned int leadingZero(const unsigned int input)
+{
+	unsigned int l;
+	const static unsigned int leadingZero8bit[256] = {8,7,6,6,5,5,5,5,4,4,4,4,4,4,4,4,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,
+											 2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,
+											 1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
+											 1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
+											 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+											 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+											 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+											 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0};
+
+	if (input & 0xFFFF0000) {
+		if (input & 0xFF000000) {
+			l = leadingZero8bit[input >> 24];
+		} else {
+			l = 8 + leadingZero8bit[input >> 16];
+		}
+	} else {
+		if (input & 0x0000FF00) {
+			l = 16 + leadingZero8bit[input >> 8];
+		} else {
+			l = 24 + leadingZero8bit[input];
+		}
+	}
+	return l;
+
+}
+// for BitPerBytePackedChar()
+static unsigned int ceilLog2(const unsigned int input)
+{
+	if (input <= 1) return 0;
+	return BITS_IN_WORD - leadingZero(input - 1);
+
+}
+// for ConvertBytePackedToWordPacked()
+static unsigned int BitPerBytePackedChar(const unsigned int alphabetSize)
+{
+	unsigned int bitPerChar;
+	bitPerChar = ceilLog2(alphabetSize);
+	// Return the largest number of bit that does not affect packing efficiency
+	if (BITS_IN_BYTE / (BITS_IN_BYTE / bitPerChar) > bitPerChar)
+		bitPerChar = BITS_IN_BYTE / (BITS_IN_BYTE / bitPerChar);
+	return bitPerChar;
+}
+// for ConvertBytePackedToWordPacked()
+static unsigned int BitPerWordPackedChar(const unsigned int alphabetSize)
+{
+	return ceilLog2(alphabetSize);
+}
+
+static void ConvertBytePackedToWordPacked(const unsigned char *input, unsigned int *output, const unsigned int alphabetSize,
+										  const unsigned int textLength)
+{
+	unsigned int i, j, k;
+	unsigned int c;
+	unsigned int bitPerBytePackedChar;
+	unsigned int bitPerWordPackedChar;
+	unsigned int charPerWord;
+	unsigned int charPerByte;
+	unsigned int bytePerIteration;
+	unsigned int byteProcessed = 0;
+	unsigned int wordProcessed = 0;
+	unsigned int mask, shift;
+	
+	unsigned int buffer[BITS_IN_WORD];
+
+	bitPerBytePackedChar = BitPerBytePackedChar(alphabetSize);
+	bitPerWordPackedChar = BitPerWordPackedChar(alphabetSize);
+	charPerByte = BITS_IN_BYTE / bitPerBytePackedChar;
+	charPerWord = BITS_IN_WORD / bitPerWordPackedChar;
+
+	bytePerIteration = charPerWord / charPerByte;
+	mask = truncateRight(ALL_ONE_MASK, BITS_IN_WORD - bitPerWordPackedChar);
+	shift = BITS_IN_WORD - BITS_IN_BYTE + bitPerBytePackedChar - bitPerWordPackedChar;
+
+	while ((wordProcessed + 1) * charPerWord < textLength) {
+
+		k = 0;
+		for (i=0; i<bytePerIteration; i++) {
+			c = (unsigned int)input[byteProcessed] << shift;
+			for (j=0; j<charPerByte; j++) {
+				buffer[k] = c & mask;
+				c <<= bitPerBytePackedChar;
+				k++;
+			}
+			byteProcessed++;
+		}
+
+		c = 0;
+		for (i=0; i<charPerWord; i++) {
+			c |= buffer[i] >> bitPerWordPackedChar * i;
+		}
+		output[wordProcessed] = c;
+		wordProcessed++;
+
+	}
+
+	k = 0;
+	for (i=0; i < (textLength - wordProcessed * charPerWord - 1) / charPerByte + 1; i++) {
+		c = (unsigned int)input[byteProcessed] << shift;
+		for (j=0; j<charPerByte; j++) {
+			buffer[k] = c & mask;
+			c <<= bitPerBytePackedChar;
+			k++;
+		}
+		byteProcessed++;
+	}
+
+	c = 0;
+	for (i=0; i<textLength - wordProcessed * charPerWord; i++) {
+		c |= buffer[i] >> bitPerWordPackedChar * i;
+	}
+	output[wordProcessed] = c;
+}
+
+BWT *BWTCreate(const unsigned int textLength, unsigned int *decodeTable)
+{
+	BWT *bwt;
+
+	bwt = (BWT*)calloc(1, sizeof(BWT));
+
+	bwt->textLength = 0;
+	bwt->inverseSa = 0;
+
+	bwt->cumulativeFreq = (unsigned*)calloc((ALPHABET_SIZE + 1), sizeof(unsigned int*));
+	initializeVAL(bwt->cumulativeFreq, ALPHABET_SIZE + 1, 0);
+
+	bwt->bwtSizeInWord = 0;
+	bwt->saValueOnBoundary = NULL;
+
+	// Generate decode tables
+	if (decodeTable == NULL) {
+		bwt->decodeTable = (unsigned*)calloc(DNA_OCC_CNT_TABLE_SIZE_IN_WORD, sizeof(unsigned int));
+		GenerateDNAOccCountTable(bwt->decodeTable);
+	} else {
+		bwt->decodeTable = decodeTable;
+	}
+
+	bwt->occMajorSizeInWord = BWTOccValueMajorSizeInWord(textLength);
+	bwt->occValueMajor = (unsigned*)calloc(bwt->occMajorSizeInWord, sizeof(unsigned int));
+
+	bwt->occSizeInWord = 0;
+	bwt->occValue = NULL;
+
+	bwt->saInterval = ALL_ONE_MASK;
+	bwt->saValueSize = 0;
+	bwt->saValue = NULL;
+
+	bwt->inverseSaInterval = ALL_ONE_MASK;
+	bwt->inverseSaSize = 0;
+	bwt->inverseSa = NULL;
+
+	return bwt;
+}
+
+BWTInc *BWTIncCreate(const unsigned int textLength, const float targetNBit,
+					 const unsigned int initialMaxBuildSize, const unsigned int incMaxBuildSize)
+{
+	BWTInc *bwtInc;
+	unsigned int i;
+
+	if (targetNBit == 0) {
+		fprintf(stderr, "BWTIncCreate() : targetNBit = 0!\n");
+		exit(1);
+	}
+	
+	bwtInc = (BWTInc*)calloc(1, sizeof(BWTInc));
+	bwtInc->numberOfIterationDone = 0;
+	bwtInc->bwt = BWTCreate(textLength, NULL);
+	bwtInc->initialMaxBuildSize = initialMaxBuildSize;
+	bwtInc->incMaxBuildSize = incMaxBuildSize;
+	bwtInc->targetNBit = targetNBit;
+	bwtInc->cumulativeCountInCurrentBuild = (unsigned*)calloc((ALPHABET_SIZE + 1), sizeof(unsigned int));
+	initializeVAL(bwtInc->cumulativeCountInCurrentBuild, ALPHABET_SIZE + 1, 0);
+
+	// Build frequently accessed data
+	bwtInc->packedShift = (unsigned*)calloc(CHAR_PER_WORD, sizeof(unsigned int));
+	for (i=0; i<CHAR_PER_WORD; i++) {
+		bwtInc->packedShift[i] = BITS_IN_WORD - (i+1) * BIT_PER_CHAR;
+	}
+
+	bwtInc->targetTextLength = textLength;
+	bwtInc->availableWord = (unsigned int)((textLength + OCC_INTERVAL - 1) / OCC_INTERVAL * OCC_INTERVAL / BITS_IN_WORD * bwtInc->targetNBit);
+	if (bwtInc->availableWord < BWTResidentSizeInWord(textLength) + BWTOccValueMinorSizeInWord(textLength)) {
+		fprintf(stderr, "BWTIncCreate() : targetNBit is too low!\n");
+		exit(1);
+	}
+	bwtInc->workingMemory = (unsigned*)calloc(bwtInc->availableWord, BYTES_IN_WORD);
+
+	return bwtInc;
+
+}
+// for BWTIncConstruct()
+static void BWTIncPutPackedTextToRank(const unsigned int *packedText, unsigned int* __restrict rank,
+									  unsigned int* __restrict cumulativeCount, const unsigned int numChar)
+{
+	unsigned int i, j;
+	unsigned int c, t;
+	unsigned int packedMask;
+	unsigned int rankIndex;
+	unsigned int lastWord, numCharInLastWord;
+
+	lastWord = (numChar - 1) / CHAR_PER_WORD;
+	numCharInLastWord = numChar - lastWord * CHAR_PER_WORD;
+
+	packedMask = ALL_ONE_MASK >> (BITS_IN_WORD - BIT_PER_CHAR);
+	rankIndex = numChar - 1;
+
+	t = packedText[lastWord] >> (BITS_IN_WORD - numCharInLastWord * BIT_PER_CHAR);
+	for (i=0; i<numCharInLastWord; i++) {
+		c = t & packedMask;
+		cumulativeCount[c+1]++;
+		rank[rankIndex] = c;
+		rankIndex--;
+		t >>= BIT_PER_CHAR;
+	}
+
+	for (i=lastWord; i--;) {	// loop from lastWord - 1 to 0
+		t = packedText[i];
+		for (j=0; j<CHAR_PER_WORD; j++) {
+			c = t & packedMask;
+			cumulativeCount[c+1]++;
+			rank[rankIndex] = c;
+			rankIndex--;
+			t >>= BIT_PER_CHAR;
+		}
+	}
+
+	// Convert occurrence to cumulativeCount
+	cumulativeCount[2] += cumulativeCount[1];
+	cumulativeCount[3] += cumulativeCount[2];
+	cumulativeCount[4] += cumulativeCount[3];
+}
+
+
+static void ForwardDNAAllOccCountNoLimit(const unsigned int*  dna, const unsigned int index,
+										 unsigned int* __restrict occCount, const unsigned int*  dnaDecodeTable)
+{
+	static const unsigned int truncateRightMask[16] = { 0x00000000, 0xC0000000, 0xF0000000, 0xFC000000,
+											   0xFF000000, 0xFFC00000, 0xFFF00000, 0xFFFC0000,
+											   0xFFFF0000, 0xFFFFC000, 0xFFFFF000, 0xFFFFFC00,
+											   0xFFFFFF00, 0xFFFFFFC0, 0xFFFFFFF0, 0xFFFFFFFC };
+
+	unsigned int iteration, wordToCount, charToCount;
+	unsigned int i, j, c;
+	unsigned int sum;
+
+	occCount[0] = 0;
+	occCount[1] = 0;
+	occCount[2] = 0;
+	occCount[3] = 0;
+
+	iteration = index / 256;
+	wordToCount = (index - iteration * 256) / 16;
+	charToCount = index - iteration * 256 - wordToCount * 16;
+
+	for (i=0; i<iteration; i++) {
+
+		sum = 0;
+		for (j=0; j<16; j++) {
+			sum += dnaDecodeTable[*dna >> 16];
+			sum += dnaDecodeTable[*dna & 0x0000FFFF];
+			dna++;
+		}
+		if (!DNA_OCC_SUM_EXCEPTION(sum)) {
+			occCount[0] += sum & 0x000000FF;	sum >>= 8;
+			occCount[1] += sum & 0x000000FF;	sum >>= 8;
+			occCount[2] += sum & 0x000000FF;	sum >>= 8;
+			occCount[3] += sum;
+		} else {
+			// only some or all of the 3 bits are on
+			// in reality, only one of the four cases are possible
+			if (sum == 0x00000100) {
+				occCount[0] += 256;
+			} else if (sum == 0x00010000) {
+				occCount[1] += 256;
+			} else if (sum == 0x01000000) {
+				occCount[2] += 256;
+			} else if (sum == 0x00000000) {
+				occCount[3] += 256;
+			} else {
+				fprintf(stderr, "ForwardDNAAllOccCountNoLimit(): DNA occ sum exception!\n");
+				exit(1);
+			}
+		}
+
+	}
+
+	sum = 0;
+	for (j=0; j<wordToCount; j++) {
+		sum += dnaDecodeTable[*dna >> 16];
+		sum += dnaDecodeTable[*dna & 0x0000FFFF];
+		dna++;
+	}
+
+	if (charToCount > 0) {
+		c = *dna & truncateRightMask[charToCount];	// increase count of 'a' by 16 - c;
+		sum += dnaDecodeTable[c >> 16];
+		sum += dnaDecodeTable[c & 0xFFFF];
+		sum += charToCount - 16;	// decrease count of 'a' by 16 - positionToProcess
+	}
+
+	occCount[0] += sum & 0x000000FF;	sum >>= 8;
+	occCount[1] += sum & 0x000000FF;	sum >>= 8;
+	occCount[2] += sum & 0x000000FF;	sum >>= 8;
+	occCount[3] += sum;
+}
+
+static void BWTIncBuildPackedBwt(const unsigned int *relativeRank, unsigned int* __restrict bwt, const unsigned int numChar,
+								 const unsigned int *cumulativeCount, const unsigned int *packedShift) {
+
+	unsigned int i, c, r;
+	unsigned int previousRank, currentRank;
+	unsigned int wordIndex, charIndex;
+	unsigned int inverseSa0;
+
+	inverseSa0 = previousRank = relativeRank[0];
+
+	for (i=1; i<=numChar; i++) {
+		currentRank = relativeRank[i];
+		// previousRank > cumulativeCount[c] because $ is one of the char
+		c = (previousRank > cumulativeCount[1]) + (previousRank > cumulativeCount[2]) 
+											    + (previousRank > cumulativeCount[3]);
+		// set bwt for currentRank
+		if (c > 0) {
+			// c <> 'a'
+			r = currentRank;
+			if (r > inverseSa0) {
+				// - 1 because $ at inverseSa0 is not encoded			
+				r--;
+			}
+			wordIndex = r / CHAR_PER_WORD;
+			charIndex = r - wordIndex * CHAR_PER_WORD;
+			bwt[wordIndex] |= c << packedShift[charIndex];
+		}
+		previousRank = currentRank;
+	}
+}
+
+static inline unsigned int BWTOccValueExplicit(const BWT *bwt, const unsigned int occIndexExplicit,
+											   const unsigned int character)
+{
+	unsigned int occIndexMajor;
+
+	occIndexMajor = occIndexExplicit * OCC_INTERVAL / OCC_INTERVAL_MAJOR;
+
+	if (occIndexExplicit % OCC_VALUE_PER_WORD == 0) {
+		return bwt->occValueMajor[occIndexMajor * ALPHABET_SIZE + character] +
+			   (bwt->occValue[occIndexExplicit / OCC_VALUE_PER_WORD * ALPHABET_SIZE + character] >> 16);
+
+	} else {
+		return bwt->occValueMajor[occIndexMajor * ALPHABET_SIZE + character] +
+			   (bwt->occValue[occIndexExplicit / OCC_VALUE_PER_WORD * ALPHABET_SIZE + character] & 0x0000FFFF);
+	}
+}
+
+
+static unsigned int ForwardDNAOccCount(const unsigned int*  dna, const unsigned int index, const unsigned int character,
+									   const unsigned int*  dnaDecodeTable)
+{
+	static const unsigned int truncateRightMask[16] = { 0x00000000, 0xC0000000, 0xF0000000, 0xFC000000,
+											   0xFF000000, 0xFFC00000, 0xFFF00000, 0xFFFC0000,
+											   0xFFFF0000, 0xFFFFC000, 0xFFFFF000, 0xFFFFFC00,
+											   0xFFFFFF00, 0xFFFFFFC0, 0xFFFFFFF0, 0xFFFFFFFC };
+
+	unsigned int wordToCount, charToCount;
+	unsigned int i, c;
+	unsigned int sum = 0;
+
+	wordToCount = index / 16;
+	charToCount = index - wordToCount * 16;
+
+	for (i=0; i<wordToCount; i++) {
+		sum += dnaDecodeTable[dna[i] >> 16];
+		sum += dnaDecodeTable[dna[i] & 0x0000FFFF];
+	}
+
+	if (charToCount > 0) {
+		c = dna[i] & truncateRightMask[charToCount];	// increase count of 'a' by 16 - c;
+		sum += dnaDecodeTable[c >> 16];
+		sum += dnaDecodeTable[c & 0xFFFF];
+		sum += charToCount - 16;	// decrease count of 'a' by 16 - positionToProcess
+	}
+
+	return (sum >> (character * 8)) & 0x000000FF;
+
+}
+
+static unsigned int BackwardDNAOccCount(const unsigned int*  dna, const unsigned int index, const unsigned int character,
+										const unsigned int*  dnaDecodeTable)
+{
+	static const unsigned int truncateLeftMask[16] =  { 0x00000000, 0x00000003, 0x0000000F, 0x0000003F,
+											   0x000000FF, 0x000003FF, 0x00000FFF, 0x00003FFF,
+											   0x0000FFFF, 0x0003FFFF, 0x000FFFFF, 0x003FFFFF,
+											   0x00FFFFFF, 0x03FFFFFF, 0x0FFFFFFF, 0x3FFFFFFF };
+
+	unsigned int wordToCount, charToCount;
+	unsigned int i, c;
+	unsigned int sum = 0;
+
+	wordToCount = index / 16;
+	charToCount = index - wordToCount * 16;
+
+	dna -= wordToCount + 1;
+
+	if (charToCount > 0) {
+		c = *dna & truncateLeftMask[charToCount];	// increase count of 'a' by 16 - c;
+		sum += dnaDecodeTable[c >> 16];
+		sum += dnaDecodeTable[c & 0xFFFF];
+		sum += charToCount - 16;	// decrease count of 'a' by 16 - positionToProcess
+	}
+	
+	for (i=0; i<wordToCount; i++) {
+		dna++;
+		sum += dnaDecodeTable[*dna >> 16];
+		sum += dnaDecodeTable[*dna & 0x0000FFFF];
+	}
+
+	return (sum >> (character * 8)) & 0x000000FF;
+
+}
+
+unsigned int BWTOccValue(const BWT *bwt, unsigned int index, const unsigned int character) {
+
+	unsigned int occValue;
+	unsigned int occExplicitIndex, occIndex;
+
+	// $ is supposed to be positioned at inverseSa0 but it is not encoded
+	// therefore index is subtracted by 1 for adjustment
+	if (index > bwt->inverseSa0) {
+		index--;
+	}
+
+	occExplicitIndex = (index + OCC_INTERVAL / 2 - 1) / OCC_INTERVAL;	// Bidirectional encoding
+	occIndex = occExplicitIndex * OCC_INTERVAL;
+	occValue = BWTOccValueExplicit(bwt, occExplicitIndex, character);
+
+	if (occIndex == index) {
+		return occValue;
+	}
+
+	if (occIndex < index) {
+		return occValue + ForwardDNAOccCount(bwt->bwtCode + occIndex / CHAR_PER_WORD, index - occIndex, character, bwt->decodeTable);
+	} else {
+		return occValue - BackwardDNAOccCount(bwt->bwtCode + occIndex / CHAR_PER_WORD, occIndex - index, character, bwt->decodeTable);
+	}
+
+}
+
+static unsigned int BWTIncGetAbsoluteRank(BWT *bwt, unsigned int* __restrict absoluteRank, unsigned int* __restrict seq,
+										  const unsigned int *packedText, const unsigned int numChar,
+										  const unsigned int* cumulativeCount, const unsigned int firstCharInLastIteration)
+{
+	unsigned int saIndex;
+	unsigned int lastWord;
+	unsigned int packedMask;
+	unsigned int i, j;
+	unsigned int c, t;
+	unsigned int rankIndex;
+	unsigned int shift;
+	unsigned int seqIndexFromStart[ALPHABET_SIZE];
+	unsigned int seqIndexFromEnd[ALPHABET_SIZE];
+
+	for (i=0; i<ALPHABET_SIZE; i++) {
+		seqIndexFromStart[i] = cumulativeCount[i];
+		seqIndexFromEnd[i] = cumulativeCount[i+1] - 1;
+	}
+
+	shift = BITS_IN_WORD - BIT_PER_CHAR;
+	packedMask = ALL_ONE_MASK >> shift;
+	saIndex = bwt->inverseSa0;
+	rankIndex = numChar - 1;
+
+	lastWord = numChar / CHAR_PER_WORD;
+	for (i=lastWord; i--;) {	// loop from lastWord - 1 to 0
+		t = packedText[i];
+		for (j=0; j<CHAR_PER_WORD; j++) {
+			c = t & packedMask;
+			saIndex = bwt->cumulativeFreq[c] + BWTOccValue(bwt, saIndex, c) + 1;
+			// A counting sort using the first character of suffix is done here
+			// If rank > inverseSa0 -> fill seq from end, otherwise fill seq from start -> to leave the right entry for inverseSa0
+			if (saIndex > bwt->inverseSa0) {
+				seq[seqIndexFromEnd[c]] = rankIndex;
+				absoluteRank[seqIndexFromEnd[c]] = saIndex;
+				seqIndexFromEnd[c]--;
+			} else {
+				seq[seqIndexFromStart[c]] = rankIndex;
+				absoluteRank[seqIndexFromStart[c]] = saIndex;
+				seqIndexFromStart[c]++;
+			}
+			rankIndex--;
+			t >>= BIT_PER_CHAR;
+		}
+	}
+
+	absoluteRank[seqIndexFromStart[firstCharInLastIteration]] = bwt->inverseSa0;	// representing the substring of all preceding characters
+	seq[seqIndexFromStart[firstCharInLastIteration]] = numChar;
+
+	return seqIndexFromStart[firstCharInLastIteration];
+}
+
+static void BWTIncSortKey(unsigned int* __restrict key, unsigned int* __restrict seq, const unsigned int numItem)
+{
+	#define EQUAL_KEY_THRESHOLD	4	// Partition for equal key if data array size / the number of data with equal value with pivot < EQUAL_KEY_THRESHOLD
+
+	int lowIndex, highIndex, midIndex;
+	int lowPartitionIndex, highPartitionIndex;
+	int lowStack[32], highStack[32];
+	int stackDepth;
+	int i, j;
+	unsigned int tempSeq, tempKey;
+	int numberOfEqualKey;
+
+	if (numItem < 2) return;
+
+	stackDepth = 0;
+
+    lowIndex = 0;
+    highIndex = numItem - 1;
+
+	for (;;) {
+
+		for (;;) {
+
+			// Sort small array of data
+			if (highIndex - lowIndex < BWTINC_INSERT_SORT_NUM_ITEM) {	 // Insertion sort on smallest arrays
+				for (i=lowIndex+1; i<=highIndex; i++) {
+					tempSeq = seq[i];
+					tempKey = key[i];
+					for (j = i; j > lowIndex && key[j-1] > tempKey; j--) {
+						seq[j] = seq[j-1];
+						key[j] = key[j-1];
+					}
+					if (j != i) {
+						seq[j] = tempSeq;
+						key[j] = tempKey;
+					}
+				}
+				break;
+			}
+
+			// Choose pivot as median of the lowest, middle, and highest data; sort the three data
+
+			midIndex = average(lowIndex, highIndex);
+			if (key[lowIndex] > key[midIndex]) {
+				tempSeq = seq[lowIndex];
+				tempKey = key[lowIndex];
+				seq[lowIndex] = seq[midIndex];
+				key[lowIndex] = key[midIndex];
+				seq[midIndex] = tempSeq;
+				key[midIndex] = tempKey;
+			}
+			if (key[lowIndex] > key[highIndex]) {
+				tempSeq = seq[lowIndex];
+				tempKey = key[lowIndex];
+				seq[lowIndex] = seq[highIndex];
+				key[lowIndex] = key[highIndex];
+				seq[highIndex] = tempSeq;
+				key[highIndex] = tempKey;
+			}
+			if (key[midIndex] > key[highIndex]) {
+				tempSeq = seq[midIndex];
+				tempKey = key[midIndex];
+				seq[midIndex] = seq[highIndex];
+				key[midIndex] = key[highIndex];
+				seq[highIndex] = tempSeq;
+				key[highIndex] = tempKey;
+			}
+
+			// Partition data
+
+			numberOfEqualKey = 0;
+
+			lowPartitionIndex = lowIndex + 1;
+			highPartitionIndex = highIndex - 1;
+
+			for (;;) {
+				while (lowPartitionIndex <= highPartitionIndex && key[lowPartitionIndex] <= key[midIndex]) {
+					numberOfEqualKey += (key[lowPartitionIndex] == key[midIndex]);
+					lowPartitionIndex++;
+				}
+				while (lowPartitionIndex < highPartitionIndex) {
+					if (key[midIndex] >= key[highPartitionIndex]) {
+						numberOfEqualKey += (key[midIndex] == key[highPartitionIndex]);
+						break;
+					}
+					highPartitionIndex--;
+				}
+				if (lowPartitionIndex >= highPartitionIndex) {
+					break;
+				}
+				tempSeq = seq[lowPartitionIndex];
+				tempKey = key[lowPartitionIndex];
+				seq[lowPartitionIndex] = seq[highPartitionIndex];
+				key[lowPartitionIndex] = key[highPartitionIndex];
+				seq[highPartitionIndex] = tempSeq;
+				key[highPartitionIndex] = tempKey;
+				if (highPartitionIndex == midIndex) {
+					// partition key has been moved
+					midIndex = lowPartitionIndex;
+				}
+				lowPartitionIndex++;
+				highPartitionIndex--;
+			}
+
+			// Adjust the partition index
+			highPartitionIndex = lowPartitionIndex;
+			lowPartitionIndex--;
+
+			// move the partition key to end of low partition
+			tempSeq = seq[midIndex];
+			tempKey = key[midIndex];
+			seq[midIndex] = seq[lowPartitionIndex];
+			key[midIndex] = key[lowPartitionIndex];
+			seq[lowPartitionIndex] = tempSeq;
+			key[lowPartitionIndex] = tempKey;
+
+			if (highIndex - lowIndex + BWTINC_INSERT_SORT_NUM_ITEM <= EQUAL_KEY_THRESHOLD * numberOfEqualKey) {
+
+				// Many keys = partition key; separate the equal key data from the lower partition
+		
+				midIndex = lowIndex;
+
+				for (;;) {
+					while (midIndex < lowPartitionIndex && key[midIndex] < key[lowPartitionIndex]) {
+						midIndex++;
+					}
+					while (midIndex < lowPartitionIndex && key[lowPartitionIndex] == key[lowPartitionIndex - 1]) {
+						lowPartitionIndex--;
+					}
+					if (midIndex >= lowPartitionIndex) {
+						break;
+					}
+					tempSeq = seq[midIndex];
+					tempKey = key[midIndex];
+					seq[midIndex] = seq[lowPartitionIndex - 1];
+					key[midIndex] = key[lowPartitionIndex - 1];
+					seq[lowPartitionIndex - 1] = tempSeq;
+					key[lowPartitionIndex - 1] = tempKey;
+					midIndex++;
+					lowPartitionIndex--;
+				}
+
+			}
+
+			if (lowPartitionIndex - lowIndex > highIndex - highPartitionIndex) {
+				// put the larger partition to stack
+				lowStack[stackDepth] = lowIndex;
+				highStack[stackDepth] = lowPartitionIndex - 1;
+				stackDepth++;
+				// sort the smaller partition first
+				lowIndex = highPartitionIndex;
+			} else {
+				// put the larger partition to stack
+				lowStack[stackDepth] = highPartitionIndex;
+				highStack[stackDepth] = highIndex;
+				stackDepth++;
+				// sort the smaller partition first
+				if (lowPartitionIndex > lowIndex) {
+					highIndex = lowPartitionIndex - 1;
+				} else {
+					// all keys in the partition equals to the partition key
+					break;
+				}
+			}
+			continue;
+		}
+
+		// Pop a range from stack
+		if (stackDepth > 0) {
+			stackDepth--;
+			lowIndex = lowStack[stackDepth];
+			highIndex = highStack[stackDepth];
+			continue;
+		} else return;
+	}
+}
+
+
+static void BWTIncBuildRelativeRank(unsigned int* __restrict sortedRank, unsigned int* __restrict seq,
+									unsigned int* __restrict relativeRank, const unsigned int numItem,
+									unsigned int oldInverseSa0, const unsigned int *cumulativeCount)
+{
+	unsigned int i, c;
+	unsigned int s, r;
+	unsigned int lastRank, lastIndex;
+	unsigned int oldInverseSa0RelativeRank = 0;
+	unsigned int freq;
+
+	lastIndex = numItem;
+	lastRank = sortedRank[numItem];
+	if (lastRank > oldInverseSa0) {
+		sortedRank[numItem]--;	// to prepare for merging; $ is not encoded in bwt
+	}
+	s = seq[numItem];
+	relativeRank[s] = numItem;
+	if (lastRank == oldInverseSa0) {
+		oldInverseSa0RelativeRank = numItem;
+		oldInverseSa0++;	// so that this segment of code is not run again
+		lastRank++;			// so that oldInverseSa0 become a sorted group with 1 item
+	}
+
+	c = ALPHABET_SIZE - 1;
+	freq = cumulativeCount[c];
+
+	for (i=numItem; i--;) {	// from numItem - 1 to 0
+		r = sortedRank[i];
+		if (r > oldInverseSa0) {
+			sortedRank[i]--;	// to prepare for merging; $ is not encoded in bwt
+		}
+		s = seq[i];
+		if (i < freq) {
+			if (lastIndex >= freq) {
+				lastRank++;	// to trigger the group across alphabet boundary to be split
+			}
+			c--;
+			freq = cumulativeCount[c];
+		}
+		if (r == lastRank) {
+			relativeRank[s] = lastIndex;
+		} else {
+			if (i == lastIndex - 1) {
+				if (lastIndex < numItem && (int)seq[lastIndex + 1] < 0) {
+					seq[lastIndex] = seq[lastIndex + 1] - 1;
+				} else {
+					seq[lastIndex] = (unsigned int)-1;
+				}
+			}
+			lastIndex = i;
+			lastRank = r;
+			relativeRank[s] = i;
+			if (r == oldInverseSa0) {
+				oldInverseSa0RelativeRank = i;
+				oldInverseSa0++;	// so that this segment of code is not run again
+				lastRank++;			// so that oldInverseSa0 become a sorted group with 1 item
+			}
+		}
+	}
+
+}
+
+static void BWTIncBuildBwt(unsigned int*  seq, const unsigned int *relativeRank, const unsigned int numChar,
+						   const unsigned int *cumulativeCount)
+{
+	unsigned int i, c;
+	unsigned int previousRank, currentRank;
+
+	previousRank = relativeRank[0];
+
+	for (i=1; i<=numChar; i++) {
+		currentRank = relativeRank[i];
+		c = (previousRank >= cumulativeCount[1]) + (previousRank >= cumulativeCount[2])
+											  	 + (previousRank >= cumulativeCount[3]);
+		seq[currentRank] = c;
+		previousRank = currentRank;
+	}
+}
+
+static void BWTIncMergeBwt(const unsigned int *sortedRank, const unsigned int* oldBwt, const unsigned int *insertBwt,
+						   unsigned int* __restrict mergedBwt, const unsigned int numOldBwt, const unsigned int numInsertBwt)
+{
+	unsigned int bitsInWordMinusBitPerChar;
+	unsigned int leftShift, rightShift;
+	unsigned int o;
+	unsigned int oIndex, iIndex, mIndex;
+	unsigned int mWord, mChar, oWord, oChar;
+	unsigned int numInsert;
+
+	bitsInWordMinusBitPerChar = BITS_IN_WORD - BIT_PER_CHAR;
+
+	oIndex = 0;
+	iIndex = 0;
+	mIndex = 0;
+
+	mWord = 0;
+	mChar = 0;
+
+	mergedBwt[0] = 0;	// this can be cleared as merged Bwt slightly shift to the left in each iteration
+
+	while (oIndex < numOldBwt) {
+
+		// copy from insertBwt
+		while (iIndex <= numInsertBwt && sortedRank[iIndex] <= oIndex) {
+			if (sortedRank[iIndex] != 0) {	// special value to indicate that this is for new inverseSa0
+				mergedBwt[mWord] |= insertBwt[iIndex] << (BITS_IN_WORD - (mChar + 1) * BIT_PER_CHAR);
+				mIndex++;
+				mChar++;
+				if (mChar == CHAR_PER_WORD) {
+					mChar = 0;
+					mWord++;
+					mergedBwt[mWord] = 0;	// no need to worry about crossing mergedBwt boundary
+				}
+			}
+			iIndex++;
+		}
+
+		// Copy from oldBwt to mergedBwt
+		if (iIndex <= numInsertBwt) {
+			o = sortedRank[iIndex];
+		} else {
+			o = numOldBwt;
+		}
+		numInsert = o - oIndex;
+
+		oWord = oIndex / CHAR_PER_WORD;
+		oChar = oIndex - oWord * CHAR_PER_WORD;
+		if (oChar > mChar) {
+			leftShift = (oChar - mChar) * BIT_PER_CHAR;
+			rightShift = (CHAR_PER_WORD + mChar - oChar) * BIT_PER_CHAR;
+			mergedBwt[mWord] = mergedBwt[mWord]
+								| (oldBwt[oWord] << (oChar * BIT_PER_CHAR) >> (mChar * BIT_PER_CHAR))
+								| (oldBwt[oWord+1] >> rightShift);
+			oIndex += min(numInsert, CHAR_PER_WORD - mChar);
+			while (o > oIndex) {
+				oWord++;
+				mWord++;
+				mergedBwt[mWord] = (oldBwt[oWord] << leftShift) | (oldBwt[oWord+1] >> rightShift);
+				oIndex += CHAR_PER_WORD;
+			}
+		} else if (oChar < mChar) {
+			rightShift = (mChar - oChar) * BIT_PER_CHAR;
+			leftShift = (CHAR_PER_WORD + oChar - mChar) * BIT_PER_CHAR;
+			mergedBwt[mWord] = mergedBwt[mWord] 
+								| (oldBwt[oWord] << (oChar * BIT_PER_CHAR) >> (mChar * BIT_PER_CHAR));
+			oIndex += min(numInsert, CHAR_PER_WORD - mChar);
+			while (o > oIndex) {
+				oWord++;
+				mWord++;
+				mergedBwt[mWord] = (oldBwt[oWord-1] << leftShift) | (oldBwt[oWord] >> rightShift);
+				oIndex += CHAR_PER_WORD;
+			}
+		} else { // oChar == mChar
+			mergedBwt[mWord] = mergedBwt[mWord] | truncateLeft(oldBwt[oWord], mChar * BIT_PER_CHAR);
+			oIndex += min(numInsert, CHAR_PER_WORD - mChar);
+			while (o > oIndex) {
+				oWord++;
+				mWord++;
+				mergedBwt[mWord] = oldBwt[oWord];
+				oIndex += CHAR_PER_WORD;
+			}
+		}
+		oIndex = o;
+		mIndex += numInsert;
+
+		// Clear the trailing garbage in mergedBwt
+		mWord = mIndex / CHAR_PER_WORD;
+		mChar = mIndex - mWord * CHAR_PER_WORD;
+		if (mChar == 0) {
+			mergedBwt[mWord] = 0;
+		} else {
+			mergedBwt[mWord] = truncateRight(mergedBwt[mWord], (BITS_IN_WORD - mChar * BIT_PER_CHAR));
+		}
+
+	}
+
+	// copy from insertBwt
+	while (iIndex <= numInsertBwt) {
+		if (sortedRank[iIndex] != 0) {
+			mergedBwt[mWord] |= insertBwt[iIndex] << (BITS_IN_WORD - (mChar + 1) * BIT_PER_CHAR);
+			mIndex++;
+			mChar++;
+			if (mChar == CHAR_PER_WORD) {
+				mChar = 0;
+				mWord++;
+				mergedBwt[mWord] = 0;	// no need to worry about crossing mergedBwt boundary
+			}
+		}
+		iIndex++;
+	}
+}
+
+void BWTClearTrailingBwtCode(BWT *bwt)
+{
+	unsigned int bwtResidentSizeInWord;
+	unsigned int wordIndex, offset;
+	unsigned int i;
+
+	bwtResidentSizeInWord = BWTResidentSizeInWord(bwt->textLength);
+
+	wordIndex = bwt->textLength / CHAR_PER_WORD;
+	offset = (bwt->textLength - wordIndex * CHAR_PER_WORD) * BIT_PER_CHAR;
+	if (offset > 0) {
+		bwt->bwtCode[wordIndex] = truncateRight(bwt->bwtCode[wordIndex], BITS_IN_WORD - offset);
+	} else {
+		if (wordIndex < bwtResidentSizeInWord) {
+			bwt->bwtCode[wordIndex] = 0;
+		}
+	}
+
+	for (i=wordIndex+1; i<bwtResidentSizeInWord; i++) {
+		bwt->bwtCode[i] = 0;
+	}
+}
+
+
+void BWTGenerateOccValueFromBwt(const unsigned int*  bwt, unsigned int* __restrict occValue,
+								unsigned int* __restrict occValueMajor,
+								const unsigned int textLength, const unsigned int*  decodeTable)
+{
+	unsigned int numberOfOccValueMajor, numberOfOccValue;
+	unsigned int wordBetweenOccValue;
+	unsigned int numberOfOccIntervalPerMajor;
+	unsigned int c;
+	unsigned int i, j;
+	unsigned int occMajorIndex;
+	unsigned int occIndex, bwtIndex;
+	unsigned int sum;
+	unsigned int tempOccValue0[ALPHABET_SIZE], tempOccValue1[ALPHABET_SIZE];
+
+	wordBetweenOccValue = OCC_INTERVAL / CHAR_PER_WORD;
+
+	// Calculate occValue
+	// [lh3] by default: OCC_INTERVAL_MAJOR=65536, OCC_INTERVAL=256
+	numberOfOccValue = (textLength + OCC_INTERVAL - 1) / OCC_INTERVAL + 1;				// Value at both end for bi-directional encoding
+	numberOfOccIntervalPerMajor = OCC_INTERVAL_MAJOR / OCC_INTERVAL;
+	numberOfOccValueMajor = (numberOfOccValue + numberOfOccIntervalPerMajor - 1) / numberOfOccIntervalPerMajor;
+
+	tempOccValue0[0] = 0;
+	tempOccValue0[1] = 0;
+	tempOccValue0[2] = 0;
+	tempOccValue0[3] = 0;
+	occValueMajor[0] = 0;
+	occValueMajor[1] = 0;
+	occValueMajor[2] = 0;
+	occValueMajor[3] = 0;
+
+	occIndex = 0;
+	bwtIndex = 0;
+	for (occMajorIndex=1; occMajorIndex<numberOfOccValueMajor; occMajorIndex++) {
+
+		for (i=0; i<numberOfOccIntervalPerMajor/2; i++) {
+
+			sum = 0;
+			tempOccValue1[0] = tempOccValue0[0];
+			tempOccValue1[1] = tempOccValue0[1];
+			tempOccValue1[2] = tempOccValue0[2];
+			tempOccValue1[3] = tempOccValue0[3];
+
+			for (j=0; j<wordBetweenOccValue; j++) {
+				c = bwt[bwtIndex];
+				sum += decodeTable[c >> 16];
+				sum += decodeTable[c & 0x0000FFFF];
+				bwtIndex++;
+			}
+			if (!DNA_OCC_SUM_EXCEPTION(sum)) {
+				tempOccValue1[0] += (sum & 0x000000FF);	sum >>= 8;
+				tempOccValue1[1] += (sum & 0x000000FF);	sum >>= 8;
+				tempOccValue1[2] += (sum & 0x000000FF);	sum >>= 8;
+				tempOccValue1[3] += sum;
+			} else {
+				if (sum == 0x00000100) {
+					tempOccValue1[0] += 256;
+				} else if (sum == 0x00010000) {
+					tempOccValue1[1] += 256;
+				} else if (sum == 0x01000000) {
+					tempOccValue1[2] += 256;
+				} else {
+					tempOccValue1[3] += 256;
+				}
+			}
+			occValue[occIndex * 4 + 0] = (tempOccValue0[0] << 16) | tempOccValue1[0];
+			occValue[occIndex * 4 + 1] = (tempOccValue0[1] << 16) | tempOccValue1[1];
+			occValue[occIndex * 4 + 2] = (tempOccValue0[2] << 16) | tempOccValue1[2];
+			occValue[occIndex * 4 + 3] = (tempOccValue0[3] << 16) | tempOccValue1[3];
+			tempOccValue0[0] = tempOccValue1[0];
+			tempOccValue0[1] = tempOccValue1[1];
+			tempOccValue0[2] = tempOccValue1[2];
+			tempOccValue0[3] = tempOccValue1[3];
+			sum = 0;
+
+			occIndex++;
+
+			for (j=0; j<wordBetweenOccValue; j++) {
+				c = bwt[bwtIndex];
+				sum += decodeTable[c >> 16];
+				sum += decodeTable[c & 0x0000FFFF];
+				bwtIndex++;
+			}
+			if (!DNA_OCC_SUM_EXCEPTION(sum)) {
+				tempOccValue0[0] += (sum & 0x000000FF);	sum >>= 8;
+				tempOccValue0[1] += (sum & 0x000000FF);	sum >>= 8;
+				tempOccValue0[2] += (sum & 0x000000FF);	sum >>= 8;
+				tempOccValue0[3] += sum;
+			} else {
+				if (sum == 0x00000100) {
+					tempOccValue0[0] += 256;
+				} else if (sum == 0x00010000) {
+					tempOccValue0[1] += 256;
+				} else if (sum == 0x01000000) {
+					tempOccValue0[2] += 256;
+				} else {
+					tempOccValue0[3] += 256;
+				}
+			}
+		}
+
+		occValueMajor[occMajorIndex * 4 + 0] = occValueMajor[(occMajorIndex - 1) * 4 + 0] + tempOccValue0[0];
+		occValueMajor[occMajorIndex * 4 + 1] = occValueMajor[(occMajorIndex - 1) * 4 + 1] + tempOccValue0[1];
+		occValueMajor[occMajorIndex * 4 + 2] = occValueMajor[(occMajorIndex - 1) * 4 + 2] + tempOccValue0[2];
+		occValueMajor[occMajorIndex * 4 + 3] = occValueMajor[(occMajorIndex - 1) * 4 + 3] + tempOccValue0[3];
+		tempOccValue0[0] = 0;
+		tempOccValue0[1] = 0;
+		tempOccValue0[2] = 0;
+		tempOccValue0[3] = 0;
+
+	}
+
+	while (occIndex < (numberOfOccValue-1)/2) {
+		sum = 0;
+		tempOccValue1[0] = tempOccValue0[0];
+		tempOccValue1[1] = tempOccValue0[1];
+		tempOccValue1[2] = tempOccValue0[2];
+		tempOccValue1[3] = tempOccValue0[3];
+		for (j=0; j<wordBetweenOccValue; j++) {
+			c = bwt[bwtIndex];
+			sum += decodeTable[c >> 16];
+			sum += decodeTable[c & 0x0000FFFF];
+			bwtIndex++;
+		}
+		if (!DNA_OCC_SUM_EXCEPTION(sum)) {
+			tempOccValue1[0] += (sum & 0x000000FF);	sum >>= 8;
+			tempOccValue1[1] += (sum & 0x000000FF);	sum >>= 8;
+			tempOccValue1[2] += (sum & 0x000000FF);	sum >>= 8;
+			tempOccValue1[3] += sum;
+		} else {
+			if (sum == 0x00000100) {
+				tempOccValue1[0] += 256;
+			} else if (sum == 0x00010000) {
+				tempOccValue1[1] += 256;
+			} else if (sum == 0x01000000) {
+				tempOccValue1[2] += 256;
+			} else {
+				tempOccValue1[3] += 256;
+			}
+		}
+		occValue[occIndex * 4 + 0] = (tempOccValue0[0] << 16) | tempOccValue1[0];
+		occValue[occIndex * 4 + 1] = (tempOccValue0[1] << 16) | tempOccValue1[1];
+		occValue[occIndex * 4 + 2] = (tempOccValue0[2] << 16) | tempOccValue1[2];
+		occValue[occIndex * 4 + 3] = (tempOccValue0[3] << 16) | tempOccValue1[3];
+		tempOccValue0[0] = tempOccValue1[0];
+		tempOccValue0[1] = tempOccValue1[1];
+		tempOccValue0[2] = tempOccValue1[2];
+		tempOccValue0[3] = tempOccValue1[3];
+		sum = 0;
+		occIndex++;
+
+		for (j=0; j<wordBetweenOccValue; j++) {
+			c = bwt[bwtIndex];
+			sum += decodeTable[c >> 16];
+			sum += decodeTable[c & 0x0000FFFF];
+			bwtIndex++;
+		}
+		if (!DNA_OCC_SUM_EXCEPTION(sum)) {
+			tempOccValue0[0] += (sum & 0x000000FF);	sum >>= 8;
+			tempOccValue0[1] += (sum & 0x000000FF);	sum >>= 8;
+			tempOccValue0[2] += (sum & 0x000000FF);	sum >>= 8;
+			tempOccValue0[3] += sum;
+		} else {
+			if (sum == 0x00000100) {
+				tempOccValue0[0] += 256;
+			} else if (sum == 0x00010000) {
+				tempOccValue0[1] += 256;
+			} else if (sum == 0x01000000) {
+				tempOccValue0[2] += 256;
+			} else {
+				tempOccValue0[3] += 256;
+			}
+		}
+	}
+
+	sum = 0;
+	tempOccValue1[0] = tempOccValue0[0];
+	tempOccValue1[1] = tempOccValue0[1];
+	tempOccValue1[2] = tempOccValue0[2];
+	tempOccValue1[3] = tempOccValue0[3];
+
+	if (occIndex * 2 < numberOfOccValue - 1) {
+		for (j=0; j<wordBetweenOccValue; j++) {
+			c = bwt[bwtIndex];
+			sum += decodeTable[c >> 16];
+			sum += decodeTable[c & 0x0000FFFF];
+			bwtIndex++;
+		}
+		if (!DNA_OCC_SUM_EXCEPTION(sum)) {
+			tempOccValue1[0] += (sum & 0x000000FF);	sum >>= 8;
+			tempOccValue1[1] += (sum & 0x000000FF);	sum >>= 8;
+			tempOccValue1[2] += (sum & 0x000000FF);	sum >>= 8;
+			tempOccValue1[3] += sum;
+		} else {
+			if (sum == 0x00000100) {
+				tempOccValue1[0] += 256;
+			} else if (sum == 0x00010000) {
+				tempOccValue1[1] += 256;
+			} else if (sum == 0x01000000) {
+				tempOccValue1[2] += 256;
+			} else {
+				tempOccValue1[3] += 256;
+			}
+		}
+	}
+
+	occValue[occIndex * 4 + 0] = (tempOccValue0[0] << 16) | tempOccValue1[0];
+	occValue[occIndex * 4 + 1] = (tempOccValue0[1] << 16) | tempOccValue1[1];
+	occValue[occIndex * 4 + 2] = (tempOccValue0[2] << 16) | tempOccValue1[2];
+	occValue[occIndex * 4 + 3] = (tempOccValue0[3] << 16) | tempOccValue1[3];
+
+}
+
+static void BWTIncConstruct(BWTInc *bwtInc, const unsigned int numChar)
+{
+	unsigned int i;
+	unsigned int mergedBwtSizeInWord, mergedOccSizeInWord;
+	unsigned int firstCharInThisIteration;
+
+	unsigned int *relativeRank, *seq, *sortedRank, *insertBwt, *mergedBwt;
+	unsigned int newInverseSa0RelativeRank, oldInverseSa0RelativeRank, newInverseSa0;
+
+	#ifdef DEBUG
+	if (numChar > bwtInc->buildSize) {
+		fprintf(stderr, "BWTIncConstruct(): numChar > buildSize!\n");
+		exit(1);
+	}
+	#endif
+
+	mergedBwtSizeInWord = BWTResidentSizeInWord(bwtInc->bwt->textLength + numChar);
+	mergedOccSizeInWord = BWTOccValueMinorSizeInWord(bwtInc->bwt->textLength + numChar);
+
+	initializeVAL(bwtInc->cumulativeCountInCurrentBuild, ALPHABET_SIZE + 1, 0);
+
+	if (bwtInc->bwt->textLength == 0) {		// Initial build
+
+		// Set address
+		seq = bwtInc->workingMemory;
+		relativeRank = seq + bwtInc->buildSize + 1;
+		mergedBwt = insertBwt = bwtInc->workingMemory + bwtInc->availableWord - mergedBwtSizeInWord;	// build in place
+
+		BWTIncPutPackedTextToRank(bwtInc->packedText, relativeRank, bwtInc->cumulativeCountInCurrentBuild, numChar);
+
+		firstCharInThisIteration = relativeRank[0];
+		relativeRank[numChar] = 0;
+
+		// Sort suffix
+		QSufSortSuffixSort((int*)relativeRank, (int*)seq, (int)numChar, (int)ALPHABET_SIZE - 1, 0, FALSE);
+		newInverseSa0 = relativeRank[0];
+
+		// Clear BWT area
+		initializeVAL(insertBwt, mergedBwtSizeInWord, 0);
+
+		// Build BWT
+		BWTIncBuildPackedBwt(relativeRank, insertBwt, numChar, bwtInc->cumulativeCountInCurrentBuild, bwtInc->packedShift);
+
+		// so that the cumulativeCount is not deducted
+		bwtInc->firstCharInLastIteration = ALPHABET_SIZE;
+
+	} else {		// Incremental build
+		// Set address
+		sortedRank = bwtInc->workingMemory;
+		seq = sortedRank + bwtInc->buildSize + 1;
+		insertBwt = seq;
+		relativeRank = seq + bwtInc->buildSize + 1;
+
+		// Store the first character of this iteration
+		firstCharInThisIteration = bwtInc->packedText[0] >> (BITS_IN_WORD - BIT_PER_CHAR);
+
+		// Count occurrence of input text
+		ForwardDNAAllOccCountNoLimit(bwtInc->packedText, numChar, bwtInc->cumulativeCountInCurrentBuild + 1, bwtInc->bwt->decodeTable);
+		// Add the first character of the previous iteration to represent the inverseSa0 of the previous iteration
+		bwtInc->cumulativeCountInCurrentBuild[bwtInc->firstCharInLastIteration + 1]++;
+		bwtInc->cumulativeCountInCurrentBuild[2] += bwtInc->cumulativeCountInCurrentBuild[1];
+		bwtInc->cumulativeCountInCurrentBuild[3] += bwtInc->cumulativeCountInCurrentBuild[2];
+		bwtInc->cumulativeCountInCurrentBuild[4] += bwtInc->cumulativeCountInCurrentBuild[3];
+
+		// Get rank of new suffix among processed suffix
+		// The seq array is built into ALPHABET_SIZE + 2 groups; ALPHABET_SIZE groups + 1 group divided into 2 by inverseSa0 + inverseSa0 as 1 group
+		oldInverseSa0RelativeRank = BWTIncGetAbsoluteRank(bwtInc->bwt, sortedRank, seq, bwtInc->packedText, 
+														  numChar, bwtInc->cumulativeCountInCurrentBuild, bwtInc->firstCharInLastIteration);
+
+		// Sort rank by ALPHABET_SIZE + 2 groups (or ALPHABET_SIZE + 1 groups when inverseSa0 sit on the border of a group)
+		for (i=0; i<ALPHABET_SIZE; i++) {
+			if (bwtInc->cumulativeCountInCurrentBuild[i] > oldInverseSa0RelativeRank ||
+				bwtInc->cumulativeCountInCurrentBuild[i+1] <= oldInverseSa0RelativeRank) {
+				BWTIncSortKey(sortedRank + bwtInc->cumulativeCountInCurrentBuild[i], seq + bwtInc->cumulativeCountInCurrentBuild[i], bwtInc->cumulativeCountInCurrentBuild[i+1] - bwtInc->cumulativeCountInCurrentBuild[i]);
+			} else {
+				if (bwtInc->cumulativeCountInCurrentBuild[i] < oldInverseSa0RelativeRank) {
+					BWTIncSortKey(sortedRank + bwtInc->cumulativeCountInCurrentBuild[i], seq + bwtInc->cumulativeCountInCurrentBuild[i], oldInverseSa0RelativeRank - bwtInc->cumulativeCountInCurrentBuild[i]);
+				}
+				if (bwtInc->cumulativeCountInCurrentBuild[i+1] > oldInverseSa0RelativeRank + 1) {
+					BWTIncSortKey(sortedRank + oldInverseSa0RelativeRank + 1, seq + oldInverseSa0RelativeRank + 1, bwtInc->cumulativeCountInCurrentBuild[i+1] - oldInverseSa0RelativeRank - 1);
+				}
+			}
+		}
+
+		// build relative rank; sortedRank is updated for merging to cater for the fact that $ is not encoded in bwt
+		// the cumulative freq information is used to make sure that inverseSa0 and suffix beginning with different characters are kept in different unsorted groups)
+		BWTIncBuildRelativeRank(sortedRank, seq, relativeRank, numChar, bwtInc->bwt->inverseSa0, bwtInc->cumulativeCountInCurrentBuild);
+#ifdef DEBUG
+		if (relativeRank[numChar] != oldInverseSa0RelativeRank) {
+			fprintf(stderr, "BWTIncConstruct(): relativeRank[numChar] != oldInverseSa0RelativeRank!\n");
+			exit(1);
+		}
+#endif
+
+		// Sort suffix
+		QSufSortSuffixSort((int*)relativeRank, (int*)seq, (int)numChar, (int)numChar, 1, TRUE);
+
+		newInverseSa0RelativeRank = relativeRank[0];
+		newInverseSa0 = sortedRank[newInverseSa0RelativeRank] + newInverseSa0RelativeRank;
+
+		sortedRank[newInverseSa0RelativeRank] = 0;	// a special value so that this is skipped in the merged bwt
+
+		// Build BWT
+		BWTIncBuildBwt(seq, relativeRank, numChar, bwtInc->cumulativeCountInCurrentBuild);
+
+		// Merge BWT
+		mergedBwt = bwtInc->workingMemory + bwtInc->availableWord - mergedBwtSizeInWord 
+				    - bwtInc->numberOfIterationDone * OCC_INTERVAL / BIT_PER_CHAR;
+					// minus numberOfIteration * occInterval to create a buffer for merging
+		BWTIncMergeBwt(sortedRank, bwtInc->bwt->bwtCode, insertBwt, mergedBwt, bwtInc->bwt->textLength, numChar);
+
+	}
+
+	// Build auxiliary structure and update info and pointers in BWT
+	bwtInc->bwt->textLength += numChar;
+	bwtInc->bwt->bwtCode = mergedBwt;
+	bwtInc->bwt->bwtSizeInWord = mergedBwtSizeInWord;
+	bwtInc->bwt->occSizeInWord = mergedOccSizeInWord;
+	if (mergedBwt < bwtInc->workingMemory + mergedOccSizeInWord) {
+		fprintf(stderr, "BWTIncConstruct() : Not enough memory allocated!\n");
+		exit(1);
+	}
+
+	bwtInc->bwt->occValue = mergedBwt - mergedOccSizeInWord;
+
+	BWTClearTrailingBwtCode(bwtInc->bwt);
+	BWTGenerateOccValueFromBwt(bwtInc->bwt->bwtCode, bwtInc->bwt->occValue, bwtInc->bwt->occValueMajor,
+							   bwtInc->bwt->textLength, bwtInc->bwt->decodeTable);
+
+	bwtInc->bwt->inverseSa0 = newInverseSa0;
+	
+	bwtInc->bwt->cumulativeFreq[1] += bwtInc->cumulativeCountInCurrentBuild[1] - (bwtInc->firstCharInLastIteration <= 0);
+	bwtInc->bwt->cumulativeFreq[2] += bwtInc->cumulativeCountInCurrentBuild[2] - (bwtInc->firstCharInLastIteration <= 1);
+	bwtInc->bwt->cumulativeFreq[3] += bwtInc->cumulativeCountInCurrentBuild[3] - (bwtInc->firstCharInLastIteration <= 2);
+	bwtInc->bwt->cumulativeFreq[4] += bwtInc->cumulativeCountInCurrentBuild[4] - (bwtInc->firstCharInLastIteration <= 3);
+
+	bwtInc->firstCharInLastIteration = firstCharInThisIteration;
+
+	// Set build size and text address for the next build
+	BWTIncSetBuildSizeAndTextAddr(bwtInc);
+	bwtInc->numberOfIterationDone++;
+
+}
+
+BWTInc *BWTIncConstructFromPacked(const char *inputFileName, const float targetNBit,
+								  const unsigned int initialMaxBuildSize, const unsigned int incMaxBuildSize)
+{
+
+	FILE *packedFile;
+	unsigned int packedFileLen;
+	unsigned int totalTextLength;
+	unsigned int textToLoad, textSizeInByte;
+	unsigned int processedTextLength;
+	unsigned char lastByteLength;
+
+	BWTInc *bwtInc;
+
+	packedFile = (FILE*)fopen(inputFileName, "rb");
+
+	if (packedFile == NULL) {
+		fprintf(stderr, "BWTIncConstructFromPacked() : Cannot open inputFileName!\n");
+		exit(1);
+	}
+
+	fseek(packedFile, -1, SEEK_END);
+	packedFileLen = ftell(packedFile);
+	if ((int)packedFileLen < 0) {
+		fprintf(stderr, "BWTIncConstructFromPacked: Cannot determine file length!\n");
+		exit(1);
+	}
+	fread(&lastByteLength, sizeof(unsigned char), 1, packedFile);
+	totalTextLength = TextLengthFromBytePacked(packedFileLen, BIT_PER_CHAR, lastByteLength);
+
+	bwtInc = BWTIncCreate(totalTextLength, targetNBit, initialMaxBuildSize, incMaxBuildSize);
+
+	BWTIncSetBuildSizeAndTextAddr(bwtInc);
+
+	if (bwtInc->buildSize > totalTextLength) {
+		textToLoad = totalTextLength;
+	} else {
+		textToLoad = totalTextLength - ((totalTextLength - bwtInc->buildSize + CHAR_PER_WORD - 1) / CHAR_PER_WORD * CHAR_PER_WORD);
+	}
+	textSizeInByte = textToLoad / CHAR_PER_BYTE;	// excluded the odd byte
+
+	fseek(packedFile, -2, SEEK_CUR);
+	fseek(packedFile, -((int)textSizeInByte), SEEK_CUR);
+	fread(bwtInc->textBuffer, sizeof(unsigned char), textSizeInByte + 1, packedFile);
+	fseek(packedFile, -((int)textSizeInByte + 1), SEEK_CUR);
+
+	ConvertBytePackedToWordPacked(bwtInc->textBuffer, bwtInc->packedText, ALPHABET_SIZE, textToLoad);
+	BWTIncConstruct(bwtInc, textToLoad);
+
+	processedTextLength = textToLoad;
+
+	while (processedTextLength < totalTextLength) {
+		textToLoad = bwtInc->buildSize / CHAR_PER_WORD * CHAR_PER_WORD;
+		if (textToLoad > totalTextLength - processedTextLength) {
+			textToLoad = totalTextLength - processedTextLength;
+		}
+		textSizeInByte = textToLoad / CHAR_PER_BYTE;
+		fseek(packedFile, -((int)textSizeInByte), SEEK_CUR);
+		fread(bwtInc->textBuffer, sizeof(unsigned char), textSizeInByte, packedFile);
+		fseek(packedFile, -((int)textSizeInByte), SEEK_CUR);
+		ConvertBytePackedToWordPacked(bwtInc->textBuffer, bwtInc->packedText, ALPHABET_SIZE, textToLoad);
+		BWTIncConstruct(bwtInc, textToLoad);
+		processedTextLength += textToLoad;
+		if (bwtInc->numberOfIterationDone % 10 == 0) {
+			printf("[BWTIncConstructFromPacked] %u iterations done. %u characters processed.\n",
+				   bwtInc->numberOfIterationDone, processedTextLength);
+		}
+	}
+	return bwtInc;
+}
+
+void BWTFree(BWT *bwt)
+{
+	if (bwt == 0) return;
+	free(bwt->cumulativeFreq);
+	free(bwt->bwtCode);
+	free(bwt->occValue);
+	free(bwt->occValueMajor);
+	free(bwt->saValue);
+	free(bwt->inverseSa);
+	free(bwt->decodeTable);
+	free(bwt->saIndexRange);
+	free(bwt->saValueOnBoundary);
+	free(bwt);
+}
+
+void BWTIncFree(BWTInc *bwtInc)
+{
+	if (bwtInc == 0) return;
+	free(bwtInc->bwt);
+	free(bwtInc->workingMemory);
+	free(bwtInc);
+}
+
+static unsigned int BWTFileSizeInWord(const unsigned int numChar)
+{
+	// The $ in BWT at the position of inverseSa0 is not encoded
+	return (numChar + CHAR_PER_WORD - 1) / CHAR_PER_WORD;
+}
+
+void BWTSaveBwtCodeAndOcc(const BWT *bwt, const char *bwtFileName, const char *occValueFileName)
+{
+	FILE *bwtFile;
+/*	FILE *occValueFile; */
+	unsigned int bwtLength;
+
+	bwtFile = (FILE*)fopen(bwtFileName, "wb");
+	if (bwtFile == NULL) {
+		fprintf(stderr, "BWTSaveBwtCodeAndOcc(): Cannot open BWT code file!\n");
+		exit(1);
+	}
+
+	fwrite(&bwt->inverseSa0, sizeof(unsigned int), 1, bwtFile);
+	fwrite(bwt->cumulativeFreq + 1, sizeof(unsigned int), ALPHABET_SIZE, bwtFile);
+	bwtLength = BWTFileSizeInWord(bwt->textLength);
+	fwrite(bwt->bwtCode, sizeof(unsigned int), bwtLength, bwtFile);
+	fclose(bwtFile);
+/*
+	occValueFile = (FILE*)fopen(occValueFileName, "wb");
+	if (occValueFile == NULL) {
+		fprintf(stderr, "BWTSaveBwtCodeAndOcc(): Cannot open occ value file!\n");
+		exit(1);
+	}
+
+	fwrite(&bwt->inverseSa0, sizeof(unsigned int), 1, occValueFile);
+	fwrite(bwt->cumulativeFreq + 1, sizeof(unsigned int), ALPHABET_SIZE, occValueFile);
+	fwrite(bwt->occValue, sizeof(unsigned int), bwt->occSizeInWord, occValueFile);
+	fwrite(bwt->occValueMajor, sizeof(unsigned int), bwt->occMajorSizeInWord, occValueFile);
+	fclose(occValueFile);
+*/
+}
+
+void bwt_bwtgen(const char *fn_pac, const char *fn_bwt)
+{
+	BWTInc *bwtInc;
+	bwtInc = BWTIncConstructFromPacked(fn_pac, 2.5, 10000000, 10000000);
+	printf("[bwt_gen] Finished constructing BWT in %u iterations.\n", bwtInc->numberOfIterationDone);
+	BWTSaveBwtCodeAndOcc(bwtInc->bwt, fn_bwt, 0);
+	BWTIncFree(bwtInc);
+}
+
+int bwt_bwtgen_main(int argc, char *argv[])
+{
+	if (argc < 3) {
+		fprintf(stderr, "Usage: bwtgen <in.pac> <out.bwt>\n");
+		return 1;
+	}
+	bwt_bwtgen(argv[1], argv[2]);
+	return 0;
+}
+
+#ifdef MAIN_BWT_GEN
+
+int main(int argc, char *argv[])
+{
+	return bwt_bwtgen_main(argc, argv);
+}
+
+#endif