1548 lines
49 KiB
C
1548 lines
49 KiB
C
/*
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BWTConstruct.c BWT-Index Construction
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This module constructs BWT and auxiliary data structures.
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Copyright (C) 2004, Wong Chi Kwong.
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This program is free software; you can redistribute it and/or
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modify it under the terms of the GNU General Public License
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as published by the Free Software Foundation; either version 2
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of the License, or (at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with this program; if not, write to the Free Software
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Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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*/
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include "bwt_gen.h"
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#include "QSufSort.h"
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static unsigned int TextLengthFromBytePacked(unsigned int bytePackedLength, unsigned int bitPerChar,
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unsigned int lastByteLength)
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{
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if (bytePackedLength > ALL_ONE_MASK / (BITS_IN_BYTE / bitPerChar)) {
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fprintf(stderr, "TextLengthFromBytePacked(): text length > 2^32!\n");
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exit(1);
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}
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return (bytePackedLength - 1) * (BITS_IN_BYTE / bitPerChar) + lastByteLength;
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}
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static void initializeVAL(unsigned int *startAddr, const unsigned int length, const unsigned int initValue)
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{
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unsigned int i;
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for (i=0; i<length; i++) startAddr[i] = initValue;
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}
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static void GenerateDNAOccCountTable(unsigned int *dnaDecodeTable)
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{
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unsigned int i, j, c, t;
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for (i=0; i<DNA_OCC_CNT_TABLE_SIZE_IN_WORD; i++) {
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dnaDecodeTable[i] = 0;
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c = i;
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for (j=0; j<8; j++) {
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t = c & 0x00000003;
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dnaDecodeTable[i] += 1 << (t * 8);
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c >>= 2;
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}
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}
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}
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// for BWTIncCreate()
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static unsigned int BWTOccValueMajorSizeInWord(const unsigned int numChar)
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{
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unsigned int numOfOccValue;
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unsigned int numOfOccIntervalPerMajor;
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numOfOccValue = (numChar + OCC_INTERVAL - 1) / OCC_INTERVAL + 1; // Value at both end for bi-directional encoding
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numOfOccIntervalPerMajor = OCC_INTERVAL_MAJOR / OCC_INTERVAL;
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return (numOfOccValue + numOfOccIntervalPerMajor - 1) / numOfOccIntervalPerMajor * ALPHABET_SIZE;
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}
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// for BWTIncCreate()
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static unsigned int BWTOccValueMinorSizeInWord(const unsigned int numChar)
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{
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unsigned int numOfOccValue;
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numOfOccValue = (numChar + OCC_INTERVAL - 1) / OCC_INTERVAL + 1; // Value at both end for bi-directional encoding
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return (numOfOccValue + OCC_VALUE_PER_WORD - 1) / OCC_VALUE_PER_WORD * ALPHABET_SIZE;
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}
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// for BWTIncCreate()
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static unsigned int BWTResidentSizeInWord(const unsigned int numChar) {
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unsigned int numCharRoundUpToOccInterval;
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// The $ in BWT at the position of inverseSa0 is not encoded
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numCharRoundUpToOccInterval = (numChar + OCC_INTERVAL - 1) / OCC_INTERVAL * OCC_INTERVAL;
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return (numCharRoundUpToOccInterval + CHAR_PER_WORD - 1) / CHAR_PER_WORD;
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}
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static void BWTIncSetBuildSizeAndTextAddr(BWTInc *bwtInc)
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{
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unsigned int maxBuildSize;
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if (bwtInc->bwt->textLength == 0) {
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// initial build
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// Minus 2 because n+1 entries of seq and rank needed for n char
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maxBuildSize = (bwtInc->availableWord - 2 - OCC_INTERVAL / CHAR_PER_WORD)
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/ (2 * CHAR_PER_WORD + 1) * CHAR_PER_WORD;
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if (bwtInc->initialMaxBuildSize > 0) {
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bwtInc->buildSize = min(bwtInc->initialMaxBuildSize, maxBuildSize);
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} else {
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bwtInc->buildSize = maxBuildSize;
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}
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} else {
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// Minus 3 because n+1 entries of sorted rank, seq and rank needed for n char
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// Minus numberOfIterationDone because bwt slightly shift to left in each iteration
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maxBuildSize = (bwtInc->availableWord - bwtInc->bwt->bwtSizeInWord - bwtInc->bwt->occSizeInWord - 3
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- bwtInc->numberOfIterationDone * OCC_INTERVAL / BIT_PER_CHAR)
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/ 3;
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if (maxBuildSize < CHAR_PER_WORD) {
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fprintf(stderr, "BWTIncSetBuildSizeAndTextAddr(): Not enough space allocated to continue construction!\n");
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exit(1);
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}
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if (bwtInc->incMaxBuildSize > 0) {
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bwtInc->buildSize = min(bwtInc->incMaxBuildSize, maxBuildSize);
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} else {
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bwtInc->buildSize = maxBuildSize;
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}
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if (bwtInc->buildSize < CHAR_PER_WORD) {
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bwtInc->buildSize = CHAR_PER_WORD;
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}
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}
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if (bwtInc->buildSize < CHAR_PER_WORD) {
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fprintf(stderr, "BWTIncSetBuildSizeAndTextAddr(): Not enough space allocated to continue construction!\n");
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exit(1);
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}
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bwtInc->buildSize = bwtInc->buildSize / CHAR_PER_WORD * CHAR_PER_WORD;
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bwtInc->packedText = bwtInc->workingMemory + 2 * (bwtInc->buildSize + 1);
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bwtInc->textBuffer = (unsigned char*)(bwtInc->workingMemory + bwtInc->buildSize + 1);
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}
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// for ceilLog2()
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unsigned int leadingZero(const unsigned int input)
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{
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unsigned int l;
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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,
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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,
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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,
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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,
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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,
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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,
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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,
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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};
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if (input & 0xFFFF0000) {
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if (input & 0xFF000000) {
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l = leadingZero8bit[input >> 24];
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} else {
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l = 8 + leadingZero8bit[input >> 16];
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}
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} else {
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if (input & 0x0000FF00) {
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l = 16 + leadingZero8bit[input >> 8];
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} else {
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l = 24 + leadingZero8bit[input];
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}
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}
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return l;
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}
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// for BitPerBytePackedChar()
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static unsigned int ceilLog2(const unsigned int input)
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{
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if (input <= 1) return 0;
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return BITS_IN_WORD - leadingZero(input - 1);
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}
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// for ConvertBytePackedToWordPacked()
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static unsigned int BitPerBytePackedChar(const unsigned int alphabetSize)
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{
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unsigned int bitPerChar;
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bitPerChar = ceilLog2(alphabetSize);
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// Return the largest number of bit that does not affect packing efficiency
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if (BITS_IN_BYTE / (BITS_IN_BYTE / bitPerChar) > bitPerChar)
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bitPerChar = BITS_IN_BYTE / (BITS_IN_BYTE / bitPerChar);
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return bitPerChar;
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}
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// for ConvertBytePackedToWordPacked()
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static unsigned int BitPerWordPackedChar(const unsigned int alphabetSize)
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{
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return ceilLog2(alphabetSize);
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}
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static void ConvertBytePackedToWordPacked(const unsigned char *input, unsigned int *output, const unsigned int alphabetSize,
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const unsigned int textLength)
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{
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unsigned int i, j, k;
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unsigned int c;
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unsigned int bitPerBytePackedChar;
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unsigned int bitPerWordPackedChar;
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unsigned int charPerWord;
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unsigned int charPerByte;
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unsigned int bytePerIteration;
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unsigned int byteProcessed = 0;
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unsigned int wordProcessed = 0;
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unsigned int mask, shift;
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unsigned int buffer[BITS_IN_WORD];
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bitPerBytePackedChar = BitPerBytePackedChar(alphabetSize);
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bitPerWordPackedChar = BitPerWordPackedChar(alphabetSize);
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charPerByte = BITS_IN_BYTE / bitPerBytePackedChar;
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charPerWord = BITS_IN_WORD / bitPerWordPackedChar;
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bytePerIteration = charPerWord / charPerByte;
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mask = truncateRight(ALL_ONE_MASK, BITS_IN_WORD - bitPerWordPackedChar);
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shift = BITS_IN_WORD - BITS_IN_BYTE + bitPerBytePackedChar - bitPerWordPackedChar;
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while ((wordProcessed + 1) * charPerWord < textLength) {
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k = 0;
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for (i=0; i<bytePerIteration; i++) {
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c = (unsigned int)input[byteProcessed] << shift;
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for (j=0; j<charPerByte; j++) {
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buffer[k] = c & mask;
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c <<= bitPerBytePackedChar;
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k++;
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}
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byteProcessed++;
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}
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c = 0;
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for (i=0; i<charPerWord; i++) {
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c |= buffer[i] >> bitPerWordPackedChar * i;
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}
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output[wordProcessed] = c;
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wordProcessed++;
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}
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k = 0;
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for (i=0; i < (textLength - wordProcessed * charPerWord - 1) / charPerByte + 1; i++) {
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c = (unsigned int)input[byteProcessed] << shift;
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for (j=0; j<charPerByte; j++) {
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buffer[k] = c & mask;
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c <<= bitPerBytePackedChar;
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k++;
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}
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byteProcessed++;
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}
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c = 0;
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for (i=0; i<textLength - wordProcessed * charPerWord; i++) {
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c |= buffer[i] >> bitPerWordPackedChar * i;
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}
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output[wordProcessed] = c;
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}
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BWT *BWTCreate(const unsigned int textLength, unsigned int *decodeTable)
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{
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BWT *bwt;
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bwt = (BWT*)calloc(1, sizeof(BWT));
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bwt->textLength = 0;
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bwt->inverseSa = 0;
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bwt->cumulativeFreq = (unsigned*)calloc((ALPHABET_SIZE + 1), sizeof(unsigned int*));
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initializeVAL(bwt->cumulativeFreq, ALPHABET_SIZE + 1, 0);
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bwt->bwtSizeInWord = 0;
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bwt->saValueOnBoundary = NULL;
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// Generate decode tables
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if (decodeTable == NULL) {
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bwt->decodeTable = (unsigned*)calloc(DNA_OCC_CNT_TABLE_SIZE_IN_WORD, sizeof(unsigned int));
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GenerateDNAOccCountTable(bwt->decodeTable);
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} else {
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bwt->decodeTable = decodeTable;
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}
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bwt->occMajorSizeInWord = BWTOccValueMajorSizeInWord(textLength);
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bwt->occValueMajor = (unsigned*)calloc(bwt->occMajorSizeInWord, sizeof(unsigned int));
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bwt->occSizeInWord = 0;
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bwt->occValue = NULL;
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bwt->saInterval = ALL_ONE_MASK;
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bwt->saValueSize = 0;
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bwt->saValue = NULL;
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bwt->inverseSaInterval = ALL_ONE_MASK;
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bwt->inverseSaSize = 0;
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bwt->inverseSa = NULL;
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return bwt;
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}
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BWTInc *BWTIncCreate(const unsigned int textLength, const float targetNBit,
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const unsigned int initialMaxBuildSize, const unsigned int incMaxBuildSize)
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{
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BWTInc *bwtInc;
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unsigned int i;
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if (targetNBit == 0) {
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fprintf(stderr, "BWTIncCreate() : targetNBit = 0!\n");
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exit(1);
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}
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bwtInc = (BWTInc*)calloc(1, sizeof(BWTInc));
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bwtInc->numberOfIterationDone = 0;
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bwtInc->bwt = BWTCreate(textLength, NULL);
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bwtInc->initialMaxBuildSize = initialMaxBuildSize;
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bwtInc->incMaxBuildSize = incMaxBuildSize;
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bwtInc->targetNBit = targetNBit;
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bwtInc->cumulativeCountInCurrentBuild = (unsigned*)calloc((ALPHABET_SIZE + 1), sizeof(unsigned int));
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initializeVAL(bwtInc->cumulativeCountInCurrentBuild, ALPHABET_SIZE + 1, 0);
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// Build frequently accessed data
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bwtInc->packedShift = (unsigned*)calloc(CHAR_PER_WORD, sizeof(unsigned int));
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for (i=0; i<CHAR_PER_WORD; i++) {
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bwtInc->packedShift[i] = BITS_IN_WORD - (i+1) * BIT_PER_CHAR;
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}
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bwtInc->targetTextLength = textLength;
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bwtInc->availableWord = (unsigned int)((textLength + OCC_INTERVAL - 1) / OCC_INTERVAL * OCC_INTERVAL / BITS_IN_WORD * bwtInc->targetNBit);
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if (bwtInc->availableWord < BWTResidentSizeInWord(textLength) + BWTOccValueMinorSizeInWord(textLength)) {
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fprintf(stderr, "BWTIncCreate() : targetNBit is too low!\n");
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exit(1);
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}
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bwtInc->workingMemory = (unsigned*)calloc(bwtInc->availableWord, BYTES_IN_WORD);
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return bwtInc;
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}
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// for BWTIncConstruct()
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static void BWTIncPutPackedTextToRank(const unsigned int *packedText, unsigned int* __restrict rank,
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unsigned int* __restrict cumulativeCount, const unsigned int numChar)
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{
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unsigned int i, j;
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unsigned int c, t;
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unsigned int packedMask;
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unsigned int rankIndex;
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unsigned int lastWord, numCharInLastWord;
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lastWord = (numChar - 1) / CHAR_PER_WORD;
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numCharInLastWord = numChar - lastWord * CHAR_PER_WORD;
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packedMask = ALL_ONE_MASK >> (BITS_IN_WORD - BIT_PER_CHAR);
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rankIndex = numChar - 1;
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t = packedText[lastWord] >> (BITS_IN_WORD - numCharInLastWord * BIT_PER_CHAR);
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for (i=0; i<numCharInLastWord; i++) {
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c = t & packedMask;
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cumulativeCount[c+1]++;
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rank[rankIndex] = c;
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rankIndex--;
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t >>= BIT_PER_CHAR;
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}
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for (i=lastWord; i--;) { // loop from lastWord - 1 to 0
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t = packedText[i];
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for (j=0; j<CHAR_PER_WORD; j++) {
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c = t & packedMask;
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cumulativeCount[c+1]++;
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rank[rankIndex] = c;
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rankIndex--;
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t >>= BIT_PER_CHAR;
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}
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}
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// Convert occurrence to cumulativeCount
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cumulativeCount[2] += cumulativeCount[1];
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cumulativeCount[3] += cumulativeCount[2];
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cumulativeCount[4] += cumulativeCount[3];
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}
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static void ForwardDNAAllOccCountNoLimit(const unsigned int* dna, const unsigned int index,
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unsigned int* __restrict occCount, const unsigned int* dnaDecodeTable)
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{
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static const unsigned int truncateRightMask[16] = { 0x00000000, 0xC0000000, 0xF0000000, 0xFC000000,
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0xFF000000, 0xFFC00000, 0xFFF00000, 0xFFFC0000,
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0xFFFF0000, 0xFFFFC000, 0xFFFFF000, 0xFFFFFC00,
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0xFFFFFF00, 0xFFFFFFC0, 0xFFFFFFF0, 0xFFFFFFFC };
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unsigned int iteration, wordToCount, charToCount;
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unsigned int i, j, c;
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unsigned int sum;
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occCount[0] = 0;
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occCount[1] = 0;
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occCount[2] = 0;
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occCount[3] = 0;
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iteration = index / 256;
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wordToCount = (index - iteration * 256) / 16;
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charToCount = index - iteration * 256 - wordToCount * 16;
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for (i=0; i<iteration; i++) {
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sum = 0;
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for (j=0; j<16; j++) {
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sum += dnaDecodeTable[*dna >> 16];
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sum += dnaDecodeTable[*dna & 0x0000FFFF];
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dna++;
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}
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if (!DNA_OCC_SUM_EXCEPTION(sum)) {
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occCount[0] += sum & 0x000000FF; sum >>= 8;
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occCount[1] += sum & 0x000000FF; sum >>= 8;
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occCount[2] += sum & 0x000000FF; sum >>= 8;
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occCount[3] += sum;
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} else {
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// only some or all of the 3 bits are on
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// in reality, only one of the four cases are possible
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if (sum == 0x00000100) {
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occCount[0] += 256;
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} else if (sum == 0x00010000) {
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occCount[1] += 256;
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} else if (sum == 0x01000000) {
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occCount[2] += 256;
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} else if (sum == 0x00000000) {
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occCount[3] += 256;
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} else {
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fprintf(stderr, "ForwardDNAAllOccCountNoLimit(): DNA occ sum exception!\n");
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exit(1);
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}
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}
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}
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sum = 0;
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for (j=0; j<wordToCount; j++) {
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sum += dnaDecodeTable[*dna >> 16];
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sum += dnaDecodeTable[*dna & 0x0000FFFF];
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dna++;
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}
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if (charToCount > 0) {
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c = *dna & truncateRightMask[charToCount]; // increase count of 'a' by 16 - c;
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sum += dnaDecodeTable[c >> 16];
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sum += dnaDecodeTable[c & 0xFFFF];
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sum += charToCount - 16; // decrease count of 'a' by 16 - positionToProcess
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}
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occCount[0] += sum & 0x000000FF; sum >>= 8;
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occCount[1] += sum & 0x000000FF; sum >>= 8;
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occCount[2] += sum & 0x000000FF; sum >>= 8;
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occCount[3] += sum;
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}
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static void BWTIncBuildPackedBwt(const unsigned int *relativeRank, unsigned int* __restrict bwt, const unsigned int numChar,
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const unsigned int *cumulativeCount, const unsigned int *packedShift) {
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unsigned int i, c, r;
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unsigned int previousRank, currentRank;
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unsigned int wordIndex, charIndex;
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unsigned int inverseSa0;
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inverseSa0 = previousRank = relativeRank[0];
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|
|
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
|