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DNACount.c
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/*
DNACount.c DNA Count
This module contains DNA occurrence counting functions. The DNA must be
in word-packed format.
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 "DNACount.h"
#include "MiscUtilities.h"
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;
}
}
}
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;
#ifdef DEBUG
if (index >= 256) {
fprintf(stderr, "ForwardDNAOccCount() : index >= 256!\n");
exit(1);
}
#endif
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;
}
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;
#ifdef DEBUG
if (index >= 256) {
fprintf(stderr, "ForwardDNAOccCount() : index >= 256!\n");
exit(1);
}
#endif
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;
}
void ForwardDNAAllOccCount(const unsigned int* dna, const unsigned int index, unsigned int* __restrict occCount, const unsigned int* dnaDecodeTable) {
static const unsigned int truncateRightMask[16] = { 0x00000000, 0xC0000000, 0xF0000000, 0xFC000000,
0xFF000000, 0xFFC00000, 0xFFF00000, 0xFFFC0000,
0xFFFF0000, 0xFFFFC000, 0xFFFFF000, 0xFFFFFC00,
0xFFFFFF00, 0xFFFFFFC0, 0xFFFFFFF0, 0xFFFFFFFC };
unsigned int wordToCount, charToCount;
unsigned int i, c;
unsigned int sum = 0;
#ifdef DEBUG
if (index >= 256) {
fprintf(stderr, "ForwardDNAOccCount() : index >= 256!\n");
exit(1);
}
#endif
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
}
occCount[0] = sum & 0x000000FF; sum >>= 8;
occCount[1] = sum & 0x000000FF; sum >>= 8;
occCount[2] = sum & 0x000000FF; sum >>= 8;
occCount[3] = sum;
}
void BackwardDNAAllOccCount(const unsigned int* dna, const unsigned int index, unsigned int* __restrict occCount, 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;
#ifdef DEBUG
if (index >= 256) {
fprintf(stderr, "ForwardDNAOccCount() : index >= 256!\n");
exit(1);
}
#endif
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];
}
occCount[0] = sum & 0x000000FF; sum >>= 8;
occCount[1] = sum & 0x000000FF; sum >>= 8;
occCount[2] = sum & 0x000000FF; sum >>= 8;
occCount[3] = sum;
}
unsigned int Forward1OccCount(const unsigned int* bitVector, const unsigned int index, const unsigned int* dnaDecodeTable) {
static const unsigned int truncateRightMask[32] = { 0x00000000, 0x80000000, 0xC0000000, 0xE0000000, 0xF0000000, 0xF8000000, 0xFC000000, 0xFE000000,
0xFF000000, 0xFF800000, 0xFFC00000, 0xFFE00000, 0xFFF00000, 0xFFF80000, 0xFFFC0000, 0xFFFE0000,
0xFFFF0000, 0xFFFF8000, 0xFFFFC000, 0xFFFFE000, 0xFFFFF000, 0xFFFFF800, 0xFFFFFC00, 0xFFFFFE00,
0xFFFFFF00, 0xFFFFFF80, 0xFFFFFFC0, 0xFFFFFFE0, 0xFFFFFFF0, 0xFFFFFFF8, 0xFFFFFFFC, 0xFFFFFFFE};
unsigned int wordToCount, bitToCount;
unsigned int i, c;
unsigned int sum = 0;
unsigned int numberOf1;
#ifdef DEBUG
if (index >= 256) {
fprintf(stderr, "Forward1OccCount() : index >= 256!\n");
exit(1);
}
#endif
wordToCount = index / 32;
bitToCount = index - wordToCount * 32;
for (i=0; i<wordToCount; i++) {
sum += dnaDecodeTable[bitVector[i] >> 16];
sum += dnaDecodeTable[bitVector[i] & 0x0000FFFF];
}
if (bitToCount > 0) {
c = bitVector[i] & truncateRightMask[bitToCount];
sum += dnaDecodeTable[c >> 16];
sum += dnaDecodeTable[c & 0x0000FFFF];
}
sum >>= 8;
numberOf1 = sum & 0x000000FF;
sum >>= 8;
numberOf1 = sum & 0x000000FF;
sum >>= 8;
numberOf1 = sum * 2;
return numberOf1;
}
unsigned int Backward1OccCount(const unsigned int* bitVector, const unsigned int index, const unsigned int* dnaDecodeTable) {
static const unsigned int truncateLeftMask[32] = { 0x00000000, 0x00000001, 0x00000003, 0x00000007, 0x0000000F, 0x0000001F, 0x0000003F, 0x0000007F,
0x000000FF, 0x000001FF, 0x000003FF, 0x000007FF, 0x00000FFF, 0x00001FFF, 0x00003FFF, 0x00007FFF,
0x0000FFFF, 0x0001FFFF, 0x0003FFFF, 0x0007FFFF, 0x000FFFFF, 0x001FFFFF, 0x003FFFFF, 0x007FFFFF,
0x00FFFFFF, 0x01FFFFFF, 0x03FFFFFF, 0x07FFFFFF, 0x0FFFFFFF, 0x1FFFFFFF, 0x3FFFFFFF, 0x7FFFFFFF};
unsigned int wordToCount, bitToCount;
unsigned int i, c;
unsigned int sum = 0;
unsigned int numberOf1;
#ifdef DEBUG
if (index >= 256) {
fprintf(stderr, "ForwardDNAOccCount() : index >= 256!\n");
exit(1);
}
#endif
wordToCount = index / 32;
bitToCount = index - wordToCount * 32;
bitVector -= wordToCount + 1;
if (bitToCount > 0) {
c = *bitVector & truncateLeftMask[bitToCount];
sum += dnaDecodeTable[c >> 16];
sum += dnaDecodeTable[c & 0xFFFF];
}
for (i=0; i<wordToCount; i++) {
bitVector++;
sum += dnaDecodeTable[*bitVector >> 16];
sum += dnaDecodeTable[*bitVector & 0x0000FFFF];
}
sum >>= 8;
numberOf1 = sum & 0x000000FF;
sum >>= 8;
numberOf1 = sum & 0x000000FF;
sum >>= 8;
numberOf1 = sum * 2;
return numberOf1;
}
unsigned int ForwardDNAOccCountNoLimit(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 iteration, wordToCount, charToCount;
unsigned int i, j, c;
unsigned int sum;
unsigned int occCount = 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 += (sum >> (character * 8)) & 0x000000FF;
} else {
// only some or all of the 3 bits are on
// in reality, only one of the four cases are possible
if (sum == 0x00000100) {
if (character == 0) {
occCount += 256;
}
} else if (sum == 0x00010000) {
if (character == 1) {
occCount += 256;
}
} else if (sum == 0x01000000) {
if (character == 2) {
occCount += 256;
}
} else if (sum == 0x00000000) {
if (character == 3) {
occCount += 256;
}
} else {
fprintf(stderr, "ForwardDNAOccCountNoLimit(): 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 += (sum >> (character * 8)) & 0x000000FF;
return occCount;
}
unsigned int BackwardDNAOccCountNoLimit(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 iteration, wordToCount, charToCount;
unsigned int i, j, c;
unsigned int sum = 0;
unsigned int occCount;
dna -= index / 16 + 1;
iteration = index / 256;
wordToCount = (index - iteration * 256) / 16;
charToCount = index - iteration * 256 - wordToCount * 16;
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 (j=0; j<wordToCount; j++) {
dna++;
sum += dnaDecodeTable[*dna >> 16];
sum += dnaDecodeTable[*dna & 0x0000FFFF];
}
occCount = (sum >> (character * 8)) & 0x000000FF;
for (i=0; i<iteration; i++) {
sum = 0;
for (j=0; j<16; j++) {
dna++;
sum += dnaDecodeTable[*dna >> 16];
sum += dnaDecodeTable[*dna & 0x0000FFFF];
}
if (!DNA_OCC_SUM_EXCEPTION(sum)) {
occCount += (sum >> (character * 8)) & 0x000000FF;
} else {
// only some or all of the 3 bits are on
// in reality, only one of the four cases are possible
if (sum == 0x00000100) {
if (character == 0) {
occCount += 256;
}
} else if (sum == 0x00010000) {
if (character == 1) {
occCount += 256;
}
} else if (sum == 0x01000000) {
if (character == 2) {
occCount += 256;
}
} else if (sum == 0x00000000) {
if (character == 3) {
occCount += 256;
}
} else {
fprintf(stderr, "BackwardDNAOccCountNoLimit(): DNA occ sum exception!\n");
exit(1);
}
}
}
return occCount;
}
void ForwardDNAAllOccCountNoLimit(const unsigned int* dna, const unsigned int index, unsigned int* __restrict occCount, const unsigned int* dnaDecodeTable) {
static const unsigned int truncateRightMask[16] = { 0x00000000, 0xC0000000, 0xF0000000, 0xFC000000,
0xFF000000, 0xFFC00000, 0xFFF00000, 0xFFFC0000,
0xFFFF0000, 0xFFFFC000, 0xFFFFF000, 0xFFFFFC00,
0xFFFFFF00, 0xFFFFFFC0, 0xFFFFFFF0, 0xFFFFFFFC };
unsigned int iteration, wordToCount, charToCount;
unsigned int i, j, c;
unsigned int sum;
occCount[0] = 0;
occCount[1] = 0;
occCount[2] = 0;
occCount[3] = 0;
iteration = index / 256;
wordToCount = (index - iteration * 256) / 16;
charToCount = index - iteration * 256 - wordToCount * 16;
for (i=0; i<iteration; i++) {
sum = 0;
for (j=0; j<16; j++) {
sum += dnaDecodeTable[*dna >> 16];
sum += dnaDecodeTable[*dna & 0x0000FFFF];
dna++;
}
if (!DNA_OCC_SUM_EXCEPTION(sum)) {
occCount[0] += sum & 0x000000FF; sum >>= 8;
occCount[1] += sum & 0x000000FF; sum >>= 8;
occCount[2] += sum & 0x000000FF; sum >>= 8;
occCount[3] += sum;
} else {
// only some or all of the 3 bits are on
// in reality, only one of the four cases are possible
if (sum == 0x00000100) {
occCount[0] += 256;
} else if (sum == 0x00010000) {
occCount[1] += 256;
} else if (sum == 0x01000000) {
occCount[2] += 256;
} else if (sum == 0x00000000) {
occCount[3] += 256;
} else {
fprintf(stderr, "ForwardDNAAllOccCountNoLimit(): DNA occ sum exception!\n");
exit(1);
}
}
}
sum = 0;
for (j=0; j<wordToCount; j++) {
sum += dnaDecodeTable[*dna >> 16];
sum += dnaDecodeTable[*dna & 0x0000FFFF];
dna++;
}
if (charToCount > 0) {
c = *dna & truncateRightMask[charToCount]; // increase count of 'a' by 16 - c;
sum += dnaDecodeTable[c >> 16];
sum += dnaDecodeTable[c & 0xFFFF];
sum += charToCount - 16; // decrease count of 'a' by 16 - positionToProcess
}
occCount[0] += sum & 0x000000FF; sum >>= 8;
occCount[1] += sum & 0x000000FF; sum >>= 8;
occCount[2] += sum & 0x000000FF; sum >>= 8;
occCount[3] += sum;
}
void BackwardDNAAllOccCountNoLimit(const unsigned int* dna, const unsigned int index, unsigned int* __restrict occCount, 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 iteration, wordToCount, charToCount;
unsigned int i, j, c;
unsigned int sum;
dna -= index / 16 + 1;
iteration = index / 256;
wordToCount = (index - iteration * 256) / 16;
charToCount = index - iteration * 256 - wordToCount * 16;
sum = 0;
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 (j=0; j<wordToCount; j++) {
dna++;
sum += dnaDecodeTable[*dna >> 16];
sum += dnaDecodeTable[*dna & 0x0000FFFF];
}
occCount[0] = sum & 0x000000FF; sum >>= 8;
occCount[1] = sum & 0x000000FF; sum >>= 8;
occCount[2] = sum & 0x000000FF; sum >>= 8;
occCount[3] = sum;
for (i=0; i<iteration; i++) {
sum = 0;
for (j=0; j<16; j++) {
dna++;
sum += dnaDecodeTable[*dna >> 16];
sum += dnaDecodeTable[*dna & 0x0000FFFF];
}
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, "BackwardDNAAllOccCountNoLimit(): DNA occ sum exception!\n");
exit(1);
}
}
}
}
void GenerateDNA_NOccCountTable(unsigned int *dnaDecodeTable) {
unsigned int i, j, c, t;
for (i=0; i<DNA_N_OCC_CNT_TABLE_SIZE_IN_WORD; i++) {
dnaDecodeTable[i] = 0;
c = i;
for (j=0; j<5; j++) {
t = c & 0x00000007;
if (t != 4) {
// Count of 'n' is to be derived from acgt
dnaDecodeTable[i] += 1 << (t * 8);
}
c >>= 3;
}
}
}
unsigned int ForwardDNA_NOccCount(const unsigned int* dna, const unsigned int index, const unsigned int character, const unsigned int* dnaDecodeTable) {
static const unsigned int truncateRightMask[10] = { 0x00000000, 0xE0000000, 0xFC000000, 0xFF800000,
0xFFF00000, 0xFFFE0000, 0xFFFFC000, 0xFFFFF800,
0xFFFFFF00, 0xFFFFFFE0};
unsigned int wordToCount, charToCount;
unsigned int i, c;
unsigned int sum = 0;
unsigned int occCount;
#ifdef DEBUG
if (index > 250) {
fprintf(stderr, "ForwardDNA_NOccCount() : index > 250!\n");
exit(1);
}
#endif
wordToCount = index / 10;
charToCount = index - wordToCount * 10;
for (i=0; i<wordToCount; i++) {
sum += dnaDecodeTable[dna[i] >> 17];
sum += dnaDecodeTable[(dna[i] >> 2) & 0x00007FFF];
}
if (charToCount > 0) {
c = dna[i] & truncateRightMask[charToCount]; // increase count of 'a' by 10 - charToCount;
sum += dnaDecodeTable[c >> 17];
sum += dnaDecodeTable[(c >> 2) & 0x00007FFF];
sum += charToCount - 10; // decrease count of 'a' by 10 - charToCount
}
if (character != 4) {
occCount = (sum >> (character * 8)) & 0x000000FF;
} else {
occCount = index;
occCount -= sum & 0x000000FF; sum >>= 8;
occCount -= sum & 0x000000FF; sum >>= 8;
occCount -= sum & 0x000000FF; sum >>= 8;
occCount -= sum;
}
return occCount;
}
unsigned int BackwardDNA_NOccCount(const unsigned int* dna, const unsigned int index, const unsigned int character, const unsigned int* dnaDecodeTable) {
static const unsigned int truncateLeftMask[10] = { 0x00000000, 0x0000001C, 0x000000FC, 0x000007FC,
0x00003FFC, 0x0001FFFC, 0x000FFFFC, 0x007FFFFC,
0x03FFFFFC, 0x1FFFFFFC};
unsigned int wordToCount, charToCount;
unsigned int j, c;
unsigned int sum = 0;
unsigned int occCount;
#ifdef DEBUG
if (index > 250) {
fprintf(stderr, "BackwardDNA_NOccCount() : index >= 250!\n");
exit(1);
}
#endif
wordToCount = index / 10;
charToCount = index - wordToCount * 10;
dna -= wordToCount + 1;
if (charToCount > 0) {
c = *dna & truncateLeftMask[charToCount]; // increase count of 'a' by 10 - charToCount;
sum += dnaDecodeTable[c >> 17];
sum += dnaDecodeTable[(c >> 2) & 0x00007FFF];
sum += charToCount - 10; // decrease count of 'a' by 10 - charToCount
}
for (j=0; j<wordToCount; j++) {
dna++;
sum += dnaDecodeTable[*dna >> 17];
sum += dnaDecodeTable[(*dna >> 2) & 0x00007FFF];
}
if (character != 4) {
occCount = (sum >> (character * 8)) & 0x000000FF;
} else {
occCount = index;
occCount -= sum & 0x000000FF; sum >>= 8;
occCount -= sum & 0x000000FF; sum >>= 8;
occCount -= sum & 0x000000FF; sum >>= 8;
occCount -= sum;
}
#ifdef DEBUG
if (occCount > index + 1) {
fprintf(stderr, "BackwardDNA_NOccCount() : occCount > index + 1!\n");
exit(1);
}
#endif
return occCount;
}
void ForwardDNA_NAllOccCount(const unsigned int* dna, const unsigned int index, unsigned int* __restrict occCount, const unsigned int* dnaDecodeTable) {
static const unsigned int truncateRightMask[10] = { 0x00000000, 0xE0000000, 0xFC000000, 0xFF800000,
0xFFF00000, 0xFFFE0000, 0xFFFFC000, 0xFFFFF800,
0xFFFFFF00, 0xFFFFFFE0};
unsigned int wordToCount, charToCount;
unsigned int i, c;
unsigned int sum = 0;
#ifdef DEBUG
if (index > 250) {
fprintf(stderr, "ForwardDNA_NAllOccCount() : index >= 250!\n");
exit(1);
}
#endif
wordToCount = index / 10;
charToCount = index - wordToCount * 10;
for (i=0; i<wordToCount; i++) {
sum += dnaDecodeTable[dna[i] >> 17];
sum += dnaDecodeTable[(dna[i] >> 2) & 0x00007FFF];
}
if (charToCount > 0) {
c = dna[i] & truncateRightMask[charToCount]; // increase count of 'a' by 10 - charToCount;
sum += dnaDecodeTable[c >> 17];
sum += dnaDecodeTable[(c >> 2) & 0x00007FFF];
sum += charToCount - 10; // decrease count of 'a' by 10 - charToCount
}
occCount[0] = sum & 0x000000FF; sum >>= 8;
occCount[1] = sum & 0x000000FF; sum >>= 8;
occCount[2] = sum & 0x000000FF; sum >>= 8;
occCount[3] = sum;
}
void BackwardDNA_NAllOccCount(const unsigned int* dna, const unsigned int index, unsigned int* __restrict occCount, const unsigned int* dnaDecodeTable) {
static const unsigned int truncateLeftMask[10] = { 0x00000000, 0x0000001C, 0x000000FC, 0x000007FC,
0x00003FFC, 0x0001FFFC, 0x000FFFFC, 0x007FFFFC,
0x03FFFFFC, 0x1FFFFFFC};
unsigned int wordToCount, charToCount;
unsigned int j, c;
unsigned int sum = 0;
#ifdef DEBUG
if (index > 250) {
fprintf(stderr, "BackwardDNA_NAllOccCount() : index >= 250!\n");
exit(1);
}
#endif
wordToCount = index / 10;
charToCount = index - wordToCount * 10;
dna -= wordToCount + 1;
if (charToCount > 0) {
c = *dna & truncateLeftMask[charToCount]; // increase count of 'a' by 10 - charToCount;
sum += dnaDecodeTable[c >> 17];
sum += dnaDecodeTable[(c >> 2) & 0x00007FFF];
sum += charToCount - 10; // decrease count of 'a' by 16 - charToCount
}
for (j=0; j<wordToCount; j++) {
dna++;
sum += dnaDecodeTable[*dna >> 17];
sum += dnaDecodeTable[(*dna >> 2) & 0x00007FFF];
}
occCount[0] = sum & 0x000000FF; sum >>= 8;
occCount[1] = sum & 0x000000FF; sum >>= 8;
occCount[2] = sum & 0x000000FF; sum >>= 8;
occCount[3] = sum;
}
unsigned int ForwardDNA_NOccCountNoLimit(const unsigned int* dna, const unsigned int index, const unsigned int character, const unsigned int* dnaDecodeTable) {
static const unsigned int truncateRightMask[10] = { 0x00000000, 0xE0000000, 0xFC000000, 0xFF800000,
0xFFF00000, 0xFFFE0000, 0xFFFFC000, 0xFFFFF800,
0xFFFFFF00, 0xFFFFFFE0};
unsigned int iteration, wordToCount, charToCount;
unsigned int i, j, c;
unsigned int sum;
unsigned int occCount = 0;
iteration = index / 250;
wordToCount = (index - iteration * 250) / 10;
charToCount = index - iteration * 250 - wordToCount * 10;
for (i=0; i<iteration; i++) {
sum = 0;
for (j=0; j<25; j++) {
sum += dnaDecodeTable[*dna >> 17];
sum += dnaDecodeTable[(*dna >> 2) & 0x00007FFF];
dna++;
}
if (character != 4) {
occCount += (sum >> (character * 8)) & 0x000000FF;
} else {
occCount -= sum & 0x000000FF; sum >>= 8;
occCount -= sum & 0x000000FF; sum >>= 8;
occCount -= sum & 0x000000FF; sum >>= 8;
occCount -= sum;
}
}
sum = 0;
for (j=0; j<wordToCount; j++) {
sum += dnaDecodeTable[*dna >> 17];
sum += dnaDecodeTable[(*dna >> 2) & 0x00007FFF];
dna++;
}
if (charToCount > 0) {
c = *dna & truncateRightMask[charToCount]; // increase count of 'a' by 10 - charToCount;
sum += dnaDecodeTable[c >> 17];
sum += dnaDecodeTable[(c >> 2) & 0x00007FFF];
sum += charToCount - 10; // decrease count of 'a' by 10 - charToCount
}
if (character != 4) {
occCount += (sum >> (character * 8)) & 0x000000FF;
} else {
occCount += index;
occCount -= sum & 0x000000FF; sum >>= 8;
occCount -= sum & 0x000000FF; sum >>= 8;
occCount -= sum & 0x000000FF; sum >>= 8;
occCount -= sum;
}
return occCount;
}
unsigned int BackwardDNA_NOccCountNoLimit(const unsigned int* dna, const unsigned int index, const unsigned int character, const unsigned int* dnaDecodeTable) {
static const unsigned int truncateLeftMask[10] = { 0x00000000, 0x0000001C, 0x000000FC, 0x000007FC,
0x00003FFC, 0x0001FFFC, 0x000FFFFC, 0x007FFFFC,
0x03FFFFFC, 0x1FFFFFFC};
unsigned int iteration, wordToCount, charToCount;
unsigned int i, j, c;
unsigned int sum = 0;
unsigned int occCount = 0;
dna -= index / 10 + 1;
iteration = index / 250;
wordToCount = (index - iteration * 250) / 10;
charToCount = index - iteration * 250 - wordToCount * 10;
if (charToCount > 0) {
c = *dna & truncateLeftMask[charToCount]; // increase count of 'a' by 10 - charToCount;
sum += dnaDecodeTable[c >> 17];
sum += dnaDecodeTable[(c >> 2) & 0x00007FFF];
sum += charToCount - 10; // decrease count of 'a' by 10 - charToCount
}
for (j=0; j<wordToCount; j++) {
dna++;
sum += dnaDecodeTable[*dna >> 17];
sum += dnaDecodeTable[(*dna >> 2) & 0x00007FFF];
}
if (character != 4) {
occCount = (sum >> (character * 8)) & 0x000000FF;
} else {
occCount = index;
occCount -= sum & 0x000000FF; sum >>= 8;
occCount -= sum & 0x000000FF; sum >>= 8;
occCount -= sum & 0x000000FF; sum >>= 8;
occCount -= sum;
}
for (i=0; i<iteration; i++) {
sum = 0;
for (j=0; j<25; j++) {
dna++;
sum += dnaDecodeTable[*dna >> 17];
sum += dnaDecodeTable[(*dna >> 2) & 0x00007FFF];
}
if (character != 4) {
occCount += (sum >> (character * 8)) & 0x000000FF;
} else {
occCount -= sum & 0x000000FF; sum >>= 8;
occCount -= sum & 0x000000FF; sum >>= 8;
occCount -= sum & 0x000000FF; sum >>= 8;
occCount -= sum;
}
}
return occCount;
}
void ForwardDNA_NAllOccCountNoLimit(const unsigned int* dna, const unsigned int index, unsigned int* __restrict occCount, const unsigned int* dnaDecodeTable) {
static const unsigned int truncateRightMask[10] = { 0x00000000, 0xE0000000, 0xFC000000, 0xFF800000,
0xFFF00000, 0xFFFE0000, 0xFFFFC000, 0xFFFFF800,
0xFFFFFF00, 0xFFFFFFE0};
unsigned int iteration, wordToCount, charToCount;
unsigned int i, j, c;
unsigned int sum;
occCount[0] = 0;
occCount[1] = 0;
occCount[2] = 0;
occCount[3] = 0;
iteration = index / 250;
wordToCount = (index - iteration * 250) / 10;
charToCount = index - iteration * 250 - wordToCount * 10;
for (i=0; i<iteration; i++) {
sum = 0;
for (j=0; j<25; j++) {
sum += dnaDecodeTable[*dna >> 17];
sum += dnaDecodeTable[(*dna >> 2) & 0x00007FFF];
dna++;
}
occCount[0] += sum & 0x000000FF; sum >>= 8;
occCount[1] += sum & 0x000000FF; sum >>= 8;
occCount[2] += sum & 0x000000FF; sum >>= 8;
occCount[3] += sum;
}
sum = 0;
for (j=0; j<wordToCount; j++) {
sum += dnaDecodeTable[*dna >> 17];
sum += dnaDecodeTable[(*dna >> 2) & 0x00007FFF];
dna++;
}
if (charToCount > 0) {
c = *dna & truncateRightMask[charToCount]; // increase count of 'a' by 10 - charToCount;
sum += dnaDecodeTable[c >> 17];
sum += dnaDecodeTable[(c >> 2) & 0x00007FFF];
sum += charToCount - 10; // decrease count of 'a' by 10 - charToCount
}
occCount[0] += sum & 0x000000FF; sum >>= 8;
occCount[1] += sum & 0x000000FF; sum >>= 8;
occCount[2] += sum & 0x000000FF; sum >>= 8;
occCount[3] += sum;
}
void BackwardDNA_NAllOccCountNoLimit(const unsigned int* dna, const unsigned int index, unsigned int* __restrict occCount, const unsigned int* dnaDecodeTable) {
static const unsigned int truncateLeftMask[10] = { 0x00000000, 0x0000001C, 0x000000FC, 0x000007FC,
0x00003FFC, 0x0001FFFC, 0x000FFFFC, 0x007FFFFC,
0x03FFFFFC, 0x1FFFFFFC};
unsigned int iteration, wordToCount, charToCount;
unsigned int i, j, c;
unsigned int sum = 0;
dna -= index / 10 + 1;
iteration = index / 250;
wordToCount = (index - iteration * 250) / 10;
charToCount = index - iteration * 250 - wordToCount * 10;
if (charToCount > 0) {
c = *dna & truncateLeftMask[charToCount]; // increase count of 'a' by 10 - charToCount;
sum += dnaDecodeTable[c >> 17];
sum += dnaDecodeTable[(c >> 2) & 0x00007FFF];
sum += charToCount - 10; // decrease count of 'a' by 16 - charToCount
}
for (j=0; j<wordToCount; j++) {
dna++;
sum += dnaDecodeTable[*dna >> 17];
sum += dnaDecodeTable[(*dna >> 2) & 0x00007FFF];
}