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genasm_aligner_withDQ.c
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genasm_aligner_withDQ.c
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#include <stdlib.h>
#include <string.h>
#include <limits.h>
#include <stdio.h>
#include <math.h>
#include <inttypes.h>
#include <stdbool.h>
#include <ctype.h>
#include <time.h>
unsigned long long *generatePatternBitmasksACGT(char* pattern, int m)
{
int count = ceil(m/64.0);
int len = 4*count; // A,C,G,T
unsigned long long *patternBitmasks = (unsigned long long *) malloc(len * sizeof(unsigned long long));
unsigned long long max = ULLONG_MAX;
// Initialize the pattern bitmasks
for (int i=0; i < len; i++)
{
patternBitmasks[i] = max;
}
// Update the pattern bitmasks
int index;
for (int i=0; i < m; i++)
{
index = count - ((m-i-1) / 64) - 1;
if ((pattern[i] == 'A') || (pattern[i] == 'a'))
{
patternBitmasks[0*count + index] &= ~(1ULL << ((m-i-1) % 64));
}
else if ((pattern[i] == 'C') || (pattern[i] == 'c'))
{
patternBitmasks[1*count + index] &= ~(1ULL << ((m-i-1) % 64));
}
else if ((pattern[i] == 'G') || (pattern[i] == 'g'))
{
patternBitmasks[2*count + index] &= ~(1ULL << ((m-i-1) % 64));
}
else if ((pattern[i] == 'T') || (pattern[i] == 't'))
{
patternBitmasks[3*count + index] &= ~(1ULL << ((m-i-1) % 64));
}
}
return patternBitmasks;
}
void genasmTB(unsigned long long ****tracebackMatrix, int count, int W, int O, int m, int minError, int *ed, int *textConsumed, int *patternConsumed, unsigned long long mask, char *lastChar, char *lastChar2, char *lastChar3, int *charCount, int *charCount2, int *charCount3, char *CIGARstr, char *CIGARstr2, char *MD, char *text, int *countM, int *countS, int *countD, int *countI, int *countOpen, int *countExtend, bool *isFirst, int scoreS, int scoreOpen, int scoreExtend)
{
int ind;
int curPattern = m-1;
int curText = 0;
int curError = minError;
*textConsumed = 0;
*patternConsumed = 0;
while ((*textConsumed < (W-O)) && (*patternConsumed < (W-O)) && (curPattern >= 0) && (curError >= 0))
{
ind = count - (curPattern / 64) - 1;
// affine-insertion
if (*lastChar=='I' && ((tracebackMatrix[curText][curError][3][ind] & mask) == 0))
{
curPattern -= 1;
curError -= 1;
mask = 1ULL << (curPattern % 64);
if (*lastChar == 'I')
{
*charCount += 1;
*countExtend += 1;
}
else
{
if (!*isFirst)
{
sprintf(CIGARstr, "%s%d", CIGARstr, *charCount);
sprintf(CIGARstr, "%s%c", CIGARstr, *lastChar);
}
*charCount = 1;
*lastChar = 'I';
*countOpen += 1;
}
if (*lastChar2 == 'I')
{
*charCount2 += 1;
}
else
{
if (!*isFirst)
{
sprintf(CIGARstr2, "%s%d", CIGARstr2, *charCount2);
sprintf(CIGARstr2, "%s%c", CIGARstr2, *lastChar2);
}
*charCount2 = 1;
*lastChar2 = 'I';
}
*countI += 1;
*ed += 1;
*patternConsumed += 1;
}
// affine-deletion
else if (*lastChar=='D' && ((tracebackMatrix[curText][curError][2][ind] & mask) == 0))
{
curText += 1;
curError -= 1;
if (*lastChar == 'D')
{
*charCount += 1;
*countExtend += 1;
}
else
{
if (!*isFirst)
{
sprintf(CIGARstr, "%s%d", CIGARstr, *charCount);
sprintf(CIGARstr, "%s%c", CIGARstr, *lastChar);
}
*charCount = 1;
*lastChar = 'D';
*countOpen += 1;
}
if (*lastChar2 == 'D')
{
*charCount2 += 1;
}
else
{
if (!*isFirst)
{
sprintf(CIGARstr2, "%s%d", CIGARstr2, *charCount2);
sprintf(CIGARstr2, "%s%c", CIGARstr2, *lastChar2);
}
*charCount2 = 1;
*lastChar2 = 'D';
}
if (*lastChar3 == 'M')
{
sprintf(MD, "%s%d^%c", MD, *charCount3, text[curText-1]);
*lastChar3 = 'D';
*charCount3 = 0;
}
else if (*lastChar3 == 'D')
{
sprintf(MD, "%s%c", MD, text[curText-1]);
*lastChar3 = 'D';
*charCount3 = 0;
}
else
{
sprintf(MD, "%s^%c", MD, text[curText-1]);
*lastChar3 = 'D';
*charCount3 = 0;
}
*countD += 1;
*ed += 1;
*textConsumed += 1;
}
// match
else if ((tracebackMatrix[curText][curError][0][ind] & mask) == 0)
{
curText += 1;
curPattern -= 1;
mask = 1ULL << (curPattern % 64);
if (*lastChar == 'M')
{
*charCount += 1;
}
else
{
if (!*isFirst)
{
sprintf(CIGARstr, "%s%d", CIGARstr, *charCount);
sprintf(CIGARstr, "%s%c", CIGARstr, *lastChar);
}
*charCount = 1;
*lastChar = 'M';
}
if (*lastChar2 == 'M')
{
*charCount2 += 1;
}
else
{
if (!*isFirst)
{
sprintf(CIGARstr2, "%s%d", CIGARstr2, *charCount2);
sprintf(CIGARstr2, "%s%c", CIGARstr2, *lastChar2);
}
*charCount2 = 1;
*lastChar2 = 'M';
}
if (*lastChar3 == 'M')
{
*charCount3 += 1;
}
else
{
*charCount3 = 1;
*lastChar3 = 'M';
}
*countM += 1;
*textConsumed += 1;
*patternConsumed += 1;
}
// substitution
else if ((tracebackMatrix[curText][curError][1][ind] & mask) == 0)
{
curText += 1;
curPattern -= 1;
curError -= 1;
mask = 1ULL << (curPattern % 64);
if (*lastChar == 'S')
{
*charCount += 1;
}
else
{
if (!*isFirst)
{
sprintf(CIGARstr, "%s%d", CIGARstr, *charCount);
sprintf(CIGARstr, "%s%c", CIGARstr, *lastChar);
}
*charCount = 1;
*lastChar = 'S';
}
if (*lastChar2 == 'M')
{
*charCount2 += 1;
}
else
{
if (!*isFirst)
{
sprintf(CIGARstr2, "%s%d", CIGARstr2, *charCount2);
sprintf(CIGARstr2, "%s%c", CIGARstr2, *lastChar2);
}
*charCount2 = 1;
*lastChar2 = 'M';
}
if (*lastChar3 == 'M')
{
sprintf(MD, "%s%d%c", MD, *charCount3, text[curText-1]);
*lastChar3 = 'S';
*charCount3 = 0;
}
else
{
sprintf(MD, "%s%c", MD, text[curText-1]);
*lastChar3 = 'S';
*charCount3 = 0;
}
*countS += 1;
*ed += 1;
*textConsumed += 1;
*patternConsumed += 1;
}
// deletion
else if ((tracebackMatrix[curText][curError][2][ind] & mask) == 0)
{
curText += 1;
curError -= 1;
if (*lastChar == 'D')
{
*charCount += 1;
*countExtend += 1;
}
else
{
if (!*isFirst)
{
sprintf(CIGARstr, "%s%d", CIGARstr, *charCount);
sprintf(CIGARstr, "%s%c", CIGARstr, *lastChar);
}
*charCount = 1;
*lastChar = 'D';
*countOpen += 1;
}
if (*lastChar2 == 'D')
{
*charCount2 += 1;
}
else
{
if (!*isFirst)
{
sprintf(CIGARstr2, "%s%d", CIGARstr2, *charCount2);
sprintf(CIGARstr2, "%s%c", CIGARstr2, *lastChar2);
}
*charCount2 = 1;
*lastChar2 = 'D';
}
if (*lastChar3 == 'M')
{
sprintf(MD, "%s%d^%c", MD, *charCount3, text[curText-1]);
*lastChar3 = 'D';
*charCount3 = 0;
}
else if (*lastChar3 == 'D')
{
sprintf(MD, "%s%c", MD, text[curText-1]);
*lastChar3 = 'D';
*charCount3 = 0;
}
else
{
sprintf(MD, "%s^%c", MD, text[curText-1]);
*lastChar3 = 'D';
*charCount3 = 0;
}
*countD += 1;
*ed += 1;
*textConsumed += 1;
}
// insertion
else if ((tracebackMatrix[curText][curError][3][ind] & mask) == 0)
{
curPattern -= 1;
curError -= 1;
mask = 1ULL << (curPattern % 64);
if (*lastChar == 'I')
{
*charCount += 1;
*countExtend += 1;
}
else
{
if (!*isFirst)
{
sprintf(CIGARstr, "%s%d", CIGARstr, *charCount);
sprintf(CIGARstr, "%s%c", CIGARstr, *lastChar);
}
*charCount = 1;
*lastChar = 'I';
*countOpen += 1;
}
if (*lastChar2 == 'I')
{
*charCount2 += 1;
}
else
{
if (!*isFirst)
{
sprintf(CIGARstr2, "%s%d", CIGARstr2, *charCount2);
sprintf(CIGARstr2, "%s%c", CIGARstr2, *lastChar2);
}
*charCount2 = 1;
*lastChar2 = 'I';
}
*countI += 1;
*ed += 1;
*patternConsumed += 1;
}
*isFirst = false;
}
}
void genasmDC(char *text, char *pattern, int k, int W, int O, int scoreM, int scoreS, int scoreOpen, int scoreExtend)
{
int m = (int)strlen(pattern);
int n = (int)strlen(text);
unsigned long long max = ULLONG_MAX;
int ed = 0;
char CIGARstr[m+k];
strcpy(CIGARstr, "");
char CIGARstr2[m+k];
strcpy(CIGARstr2, "");
char MD[m+k];
strcpy(MD, "");
int charCount = 0;
int charCount2 = 0;
int charCount3 = 0;
char lastChar = '0';
char lastChar2 = '0';
char lastChar3 = '0';
bool isFirst = true;
int countM = 0;
int countS = 0;
int countI = 0;
int countD = 0;
int countOpen = 0;
int countExtend = 0;
int textCur = 0;
int patternCur = 0;
int textEnd = 0;
int patternEnd = 0;
//int newError = W;
int newError = 0;
if (W > k)
{
newError = k;
}
else
{
newError = W;
}
unsigned long long ****tracebackMatrix;
tracebackMatrix = (unsigned long long ****) malloc(W * sizeof(unsigned long long ***));
for (int x=0; x < W; x++)
{
tracebackMatrix[x] = (unsigned long long ***) malloc((newError + 1) * sizeof(unsigned long long **));
for (int y=0; y < (newError + 1); y++)
{
tracebackMatrix[x][y] = (unsigned long long **) malloc(4 * sizeof(unsigned long long *));
for (int z=0; z < 4; z++)
{
tracebackMatrix[x][y][z] = (unsigned long long *) malloc(ceil(W/64.0) * sizeof(unsigned long long));
}
}
}
while ((patternCur < m) && (textCur < n))
{
textEnd = textCur + W;
if (textEnd > n)
{
textEnd = n;
}
patternEnd = patternCur + W;
if (patternEnd > m)
{
patternEnd = m;
}
int n_sub = textEnd - textCur;
int m_sub = patternEnd - patternCur;
char subText[n_sub+1];
char subPattern[m_sub+1];
int y = 0;
for (int x=textCur; x < textEnd; x++)
{
subText[y++] = text[x];
}
subText[y] = '\0';
y = 0;
for (int x=patternCur; x < patternEnd; x++)
{
subPattern[y++] = pattern[x];
}
subPattern[y] = '\0';
unsigned long long *patternBitmasks = generatePatternBitmasksACGT(subPattern, m_sub);
int count = ceil(m_sub/64.0);
int rem = m_sub % 64;
unsigned long long max1;
if (rem == 0)
{
//max1 = MSB_MASK;
max1 = 1ULL << 63;
}
else
{
max1 = 1ULL << (rem-1);
}
// Initialize the bit arrays R
int len1 = (newError+1) * count;
unsigned long long R[len1];
for (int i=0; i < len1; i++)
{
R[i] = max;
}
unsigned long long oldR[len1];
unsigned long long substitution[count], insertion[count], match[count], deletion[count], curBitmask[count];
// now traverse the text in opposite direction (i.e., forward), generate partial tracebacks at each checkpoint
for (int i=n_sub-1; i >= 0; i--)
{
char c = subText[i];
if ((c == 'A') || (c == 'a') || (c == 'C') || (c == 'c') || (c == 'G') || (c == 'g') || (c == 'T') || (c == 't'))
{
// copy the content of R to oldR
for (int itR=0; itR<len1; itR++)
{
oldR[itR] = R[itR];
}
if ((c == 'A') || (c == 'a'))
{
for (int a=0; a<count; a++)
{
curBitmask[a] = patternBitmasks[0*count + a];
}
}
else if ((c == 'C') || (c == 'c'))
{
for (int a=0; a<count; a++)
{
curBitmask[a] = patternBitmasks[1*count + a];
}
}
else if ((c == 'G') || (c == 'g'))
{
for (int a=0; a<count; a++)
{
curBitmask[a] = patternBitmasks[2*count + a];
}
}
else if ((c == 'T') || (c == 't'))
{
for (int a=0; a<count; a++)
{
curBitmask[a] = patternBitmasks[3*count + a];
}
}
// update R[0] by first shifting oldR[0] and then ORing with pattern bitmask
R[0] = oldR[0] << 1;
for (int a=1; a<count; a++)
{
R[a-1] |= (oldR[a] >> 63);
R[a] = oldR[a] << 1;
}
for (int a=0; a<count; a++)
{
R[a] |= curBitmask[a];
}
for (int a=0; a<count; a++)
{
tracebackMatrix[i][0][0][a] = R[a];
tracebackMatrix[i][0][1][a] = max;
tracebackMatrix[i][0][2][a] = max;
tracebackMatrix[i][0][3][a] = max;
}
for (int d=1; d <= newError; d++)
{
int index = (d-1) * count;
for (int a=0; a<count; a++)
{
deletion[a] = oldR[index + a];
}
substitution[0] = deletion[0] << 1;
for (int a=1; a<count; a++)
{
substitution[a-1] |= (deletion[a] >> 63);
substitution[a] = deletion[a] << 1;
}
insertion[0] = R[index] << 1;
for (int a=1; a<count; a++)
{
insertion[a-1] |= (R[index+a] >> 63);
insertion[a] = R[index+a] << 1;
}
index += count;
match[0] = oldR[index] << 1;
for (int a=1; a<count; a++)
{
match[a-1] |= (oldR[index+a] >> 63);
match[a] = oldR[index+a] << 1;
}
for (int a=0; a<count; a++)
{
match[a] |= curBitmask[a];
}
for (int a=0; a<count; a++)
{
R[index+a] = deletion[a] & substitution[a] & insertion[a] & match[a];
}
for (int a=0; a<count; a++)
{
tracebackMatrix[i][d][0][a] = match[a];
tracebackMatrix[i][d][1][a] = substitution[a];
tracebackMatrix[i][d][2][a] = deletion[a];
tracebackMatrix[i][d][3][a] = insertion[a];
}
}
}
}
int minError = -1;
unsigned long long mask = max1;
for (int t=0; t <= newError; t++)
{
if ((R[t*count] & mask) == 0)
{
minError = t;
break;
}
}
if (minError == -1)
{
printf("No alignment found!\t");
free(patternBitmasks);
for (int x=0; x < W; x++)
{
for (int y=0; y < (newError + 1); y++)
{
for (int z=0; z < 4; z++)
{
free(tracebackMatrix[x][y][z]);
}
free(tracebackMatrix[x][y]);
}
free(tracebackMatrix[x]);
}
free(tracebackMatrix);
return;
}
int textConsumed;
int patternConsumed;
genasmTB(tracebackMatrix, count, W, O, m_sub, minError, &ed, &textConsumed, &patternConsumed, mask, &lastChar, &lastChar2, &lastChar3, &charCount, &charCount2, &charCount3, CIGARstr, CIGARstr2, MD, subText, &countM, &countS, &countD, &countI, &countOpen, &countExtend, &isFirst, scoreS, scoreOpen, scoreExtend);
textCur += textConsumed;
patternCur += patternConsumed;
free(patternBitmasks);
}
for (int x=0; x < W; x++)
{
for (int y=0; y < (newError + 1); y++)
{
for (int z=0; z < 4; z++)
{
free(tracebackMatrix[x][y][z]);
}
free(tracebackMatrix[x][y]);
}
free(tracebackMatrix[x]);
}
free(tracebackMatrix);
sprintf(CIGARstr, "%s%d", CIGARstr, charCount);
sprintf(CIGARstr, "%s%c", CIGARstr, lastChar);
sprintf(CIGARstr2, "%s%d", CIGARstr2, charCount2);
sprintf(CIGARstr2, "%s%c", CIGARstr2, lastChar2);
if (lastChar3 == 'M')
{
sprintf(MD, "%s%d", MD, charCount3);
}
int score = countM*scoreM-countS*scoreS-countOpen*(scoreOpen+scoreExtend)-countExtend*scoreExtend;
printf("ED:%d\tAS:%d\t%s\t%s\t%s\n", ed, score, CIGARstr, CIGARstr2, MD);
printf("#M:%d\t#S:%d\t#O:%d\t#E:%d\n", countM, countS, countOpen, countExtend);
}
void genasm_aligner(char *text, char *pattern, int k, int W, int O, int scoreM, int scoreS, int scoreOpen, int scoreExtend)
{
genasmDC(text, pattern, k, W, O, scoreM, scoreS, scoreOpen, scoreExtend);
}
int main(int argc, char * argv[])
{
struct timespec start, end;
clock_gettime(CLOCK_MONOTONIC_RAW, &start);
genasm_aligner("CCTGTTATCCTGTGTTATCCAGGT", "CCTGTTATCCTGTGCACTACCAGGT", 4, 20, 10, 1, 4, 6, 1);
clock_gettime(CLOCK_MONOTONIC_RAW, &end);
uint64_t delta_us = (end.tv_sec - start.tv_sec) * 1000000 + (end.tv_nsec - start.tv_nsec) / 1000;
printf("Time spent: %llu microseconds\n", delta_us);
return 0;
}