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bwt_gen.c
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bwt_gen.c
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/*
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 <assert.h>
#include <stdint.h>
#include <errno.h>
#include "QSufSort.h"
#ifdef USE_MALLOC_WRAPPERS
# include "malloc_wrap.h"
#endif
typedef uint64_t bgint_t;
typedef int64_t sbgint_t;
#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 MIN_AVAILABLE_WORD 0x10000
#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 BWT {
bgint_t textLength; // length of the text
bgint_t inverseSa0; // SA-1[0]
bgint_t *cumulativeFreq; // cumulative frequency
unsigned int *bwtCode; // BWT code
unsigned int *occValue; // Occurrence values stored explicitly
bgint_t *occValueMajor; // Occurrence values stored explicitly
unsigned int *decodeTable; // For decoding BWT by table lookup
bgint_t bwtSizeInWord; // Temporary variable to hold the memory allocated
bgint_t occSizeInWord; // Temporary variable to hold the memory allocated
bgint_t occMajorSizeInWord; // Temporary variable to hold the memory allocated
} BWT;
typedef struct BWTInc {
BWT *bwt;
unsigned int numberOfIterationDone;
bgint_t *cumulativeCountInCurrentBuild;
bgint_t availableWord;
bgint_t buildSize;
bgint_t initialMaxBuildSize;
bgint_t incMaxBuildSize;
unsigned int firstCharInLastIteration;
unsigned int *workingMemory;
unsigned int *packedText;
unsigned char *textBuffer;
unsigned int *packedShift;
} BWTInc;
static bgint_t TextLengthFromBytePacked(bgint_t bytePackedLength, unsigned int bitPerChar,
unsigned int lastByteLength)
{
return (bytePackedLength - 1) * (BITS_IN_BYTE / bitPerChar) + lastByteLength;
}
static void initializeVAL(unsigned int *startAddr, const bgint_t length, const unsigned int initValue)
{
bgint_t i;
for (i=0; i<length; i++) startAddr[i] = initValue;
}
static void initializeVAL_bg(bgint_t *startAddr, const bgint_t length, const bgint_t initValue)
{
bgint_t 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 bgint_t BWTOccValueMajorSizeInWord(const bgint_t numChar)
{
bgint_t numOfOccValue;
unsigned 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 bgint_t BWTOccValueMinorSizeInWord(const bgint_t numChar)
{
bgint_t 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 bgint_t BWTResidentSizeInWord(const bgint_t numChar) {
bgint_t 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)
{
bgint_t 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) * (sizeof(bgint_t) / 4))
/ (2 * CHAR_PER_WORD + 1) * CHAR_PER_WORD / (sizeof(bgint_t) / 4);
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) * (sizeof(bgint_t) / 4))
/ 3 / (sizeof(bgint_t) / 4);
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) * (sizeof(bgint_t) / 4);
bwtInc->textBuffer = (unsigned char*)(bwtInc->workingMemory + (bwtInc->buildSize + 1) * (sizeof(bgint_t) / 4));
}
// 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 bgint_t textLength)
{
bgint_t i;
unsigned int j, k, c;
unsigned int bitPerBytePackedChar;
unsigned int bitPerWordPackedChar;
unsigned int charPerWord;
unsigned int charPerByte;
unsigned int bytePerIteration;
bgint_t byteProcessed = 0;
bgint_t 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 bgint_t textLength, unsigned int *decodeTable)
{
BWT *bwt;
bwt = (BWT*)calloc(1, sizeof(BWT));
bwt->textLength = 0;
bwt->cumulativeFreq = (bgint_t*)calloc((ALPHABET_SIZE + 1), sizeof(bgint_t));
initializeVAL_bg(bwt->cumulativeFreq, ALPHABET_SIZE + 1, 0);
bwt->bwtSizeInWord = 0;
// Generate decode tables
if (decodeTable == NULL) {
bwt->decodeTable = (unsigned*)calloc(DNA_OCC_CNT_TABLE_SIZE_IN_WORD, sizeof(unsigned int));
GenerateDNAOccCountTable(bwt->decodeTable);
} else {
// FIXME Prevent BWTFree() from freeing decodeTable in this case
bwt->decodeTable = decodeTable;
}
bwt->occMajorSizeInWord = BWTOccValueMajorSizeInWord(textLength);
bwt->occValueMajor = (bgint_t*)calloc(bwt->occMajorSizeInWord, sizeof(bgint_t));
bwt->occSizeInWord = 0;
bwt->occValue = NULL;
return bwt;
}
BWTInc *BWTIncCreate(const bgint_t textLength, unsigned int initialMaxBuildSize, unsigned int incMaxBuildSize)
{
BWTInc *bwtInc;
unsigned int i, n_iter;
if (textLength < incMaxBuildSize) incMaxBuildSize = textLength;
if (textLength < initialMaxBuildSize) initialMaxBuildSize = textLength;
bwtInc = (BWTInc*)calloc(1, sizeof(BWTInc));
bwtInc->numberOfIterationDone = 0;
bwtInc->bwt = BWTCreate(textLength, NULL);
bwtInc->initialMaxBuildSize = initialMaxBuildSize;
bwtInc->incMaxBuildSize = incMaxBuildSize;
bwtInc->cumulativeCountInCurrentBuild = (bgint_t*)calloc((ALPHABET_SIZE + 1), sizeof(bgint_t));
initializeVAL_bg(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;
n_iter = (textLength - initialMaxBuildSize) / incMaxBuildSize + 1;
bwtInc->availableWord = BWTResidentSizeInWord(textLength) + BWTOccValueMinorSizeInWord(textLength) // minimal memory requirement
+ OCC_INTERVAL / BIT_PER_CHAR * n_iter * 2 * (sizeof(bgint_t) / 4) // buffer at the end of occ array
+ incMaxBuildSize/5 * 3 * (sizeof(bgint_t) / 4); // space for the 3 temporary arrays in each iteration
if (bwtInc->availableWord < MIN_AVAILABLE_WORD) bwtInc->availableWord = MIN_AVAILABLE_WORD; // lh3: otherwise segfaul when availableWord is too small
fprintf(stderr, "[%s] textLength=%ld, availableWord=%ld\n", __func__, (long)textLength, (long)bwtInc->availableWord);
bwtInc->workingMemory = (unsigned*)calloc(bwtInc->availableWord, BYTES_IN_WORD);
return bwtInc;
}
// for BWTIncConstruct()
static void BWTIncPutPackedTextToRank(const unsigned int *packedText, bgint_t* __restrict rank,
bgint_t* __restrict cumulativeCount, const bgint_t numChar)
{
bgint_t i;
unsigned int j;
unsigned int c, t;
unsigned int packedMask;
bgint_t rankIndex;
bgint_t lastWord;
unsigned int 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 bgint_t index,
bgint_t* __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 };
bgint_t iteration, i;
unsigned int wordToCount, charToCount;
unsigned int j, c, 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 bgint_t *relativeRank, unsigned int* __restrict bwt, const bgint_t numChar,
const bgint_t *cumulativeCount, const unsigned int *packedShift) {
bgint_t i, r;
unsigned int c;
bgint_t previousRank, currentRank;
bgint_t wordIndex, charIndex;
bgint_t 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 bgint_t BWTOccValueExplicit(const BWT *bwt, const bgint_t occIndexExplicit,
const unsigned int character)
{
bgint_t 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;
}
bgint_t BWTOccValue(const BWT *bwt, bgint_t index, const unsigned int character)
{
bgint_t occValue;
bgint_t 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 bgint_t BWTIncGetAbsoluteRank(BWT *bwt, bgint_t* __restrict absoluteRank, bgint_t* __restrict seq,
const unsigned int *packedText, const bgint_t numChar,
const bgint_t* cumulativeCount, const unsigned int firstCharInLastIteration)
{
bgint_t saIndex;
bgint_t lastWord;
unsigned int packedMask;
bgint_t i;
unsigned int c, t, j;
bgint_t rankIndex;
unsigned int shift;
bgint_t seqIndexFromStart[ALPHABET_SIZE];
bgint_t 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(bgint_t* __restrict key, bgint_t* __restrict seq, const bgint_t 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
int64_t lowIndex, highIndex, midIndex;
int64_t lowPartitionIndex, highPartitionIndex;
int64_t lowStack[32], highStack[32];
int stackDepth;
int64_t i, j;
bgint_t tempSeq, tempKey;
int64_t 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(bgint_t* __restrict sortedRank, bgint_t* __restrict seq,
bgint_t* __restrict relativeRank, const bgint_t numItem,
bgint_t oldInverseSa0, const bgint_t *cumulativeCount)
{
bgint_t i, c;
bgint_t s, r;
bgint_t lastRank, lastIndex;
bgint_t 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) {
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 && (sbgint_t)seq[lastIndex + 1] < 0) {
seq[lastIndex] = seq[lastIndex + 1] - 1;
} else {
seq[lastIndex] = (bgint_t)-1;
}
}
lastIndex = i;
lastRank = r;
relativeRank[s] = i;
if (r == oldInverseSa0) {
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* insertBwt, const bgint_t *relativeRank, const bgint_t numChar,
const bgint_t *cumulativeCount)
{
unsigned int c;
bgint_t i;
bgint_t previousRank, currentRank;
previousRank = relativeRank[0];
for (i=1; i<=numChar; i++) {
currentRank = relativeRank[i];
c = (previousRank >= cumulativeCount[1]) + (previousRank >= cumulativeCount[2])
+ (previousRank >= cumulativeCount[3]);
insertBwt[currentRank] = c;
previousRank = currentRank;
}
}
static void BWTIncMergeBwt(const bgint_t *sortedRank, const unsigned int* oldBwt, const unsigned int *insertBwt,
unsigned int* __restrict mergedBwt, const bgint_t numOldBwt, const bgint_t numInsertBwt)
{
bgint_t leftShift, rightShift;
bgint_t o;
bgint_t oIndex, iIndex, mIndex;
bgint_t mWord, mChar, oWord, oChar;
bgint_t numInsert;
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++;