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SirFAST.c
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SirFAST.c
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/*
* Copyright (c) <2008 - 2020>, University of Washington, Simon Fraser University, Bilkent University
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification,
* are permitted provided that the following conditions are met:
*
* Redistributions of source code must retain the above copyright notice, this list
* of conditions and the following disclaimer.
* - Redistributions in binary form must reproduce the above copyright notice, this
* list of conditions and the following disclaimer in the documentation and/or other
* materials provided with the distribution.
* - Neither the names of the University of Washington, Simon Fraser University,
* nor the names of its contributors may be
* used to endorse or promote products derived from this software without specific
* prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
* CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
* EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
* PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
* PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
* LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
* NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
/*
Authors:
Farhad Hormozdiari
Faraz Hach
Can Alkan
Emails:
farhadh AT uw DOT edu
fhach AT cs DOT sfu DOT ca
calkan AT cs DOT bilkent DOT edu DOT tr
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <dirent.h>
#include <xmmintrin.h>
#include <emmintrin.h>
#include <mmintrin.h>
#include "Common.h"
#include "Reads.h"
#include "HashTable.h"
#include "Output.h"
#include "SirFAST.h"
#include "RefGenome.h"
#define min(a,b) ((a)>(b)?(b):(a))
#define min3(a,b,c) ((a)>(b)?(b>c?c:b):(a>c?c:a))
#define CHARCODE(a) (a=='A' ? 0 : (a=='C' ? 1 : (a=='G' ? 2 : (a=='T' ? 3 : 4))))
#define MAX_REF_SIZE 18
#define KEY_LENGTH 10 // sirfast
#define KEY_LENGTH0 5 // sirfast
#define INDEL_GAP 3 // sirfast
#define EXPECTED_GAP 2 // sirfast
#define INITIAL_GAP01 -1 // sirfast
#define INITIAL_GAP12 0 // sirfast
#define INITIAL_GAP23 5 // sirfast
#define DEBUG 3
#define TEST_KEY_NUM 3
#define READ_NUM 4
int key_length[4];
int initial_gap[3];
int expected_gap[3];
double binomial_coefficient(int n, int k);
float calculateScore(int index, char *seq, char *qual, char *md);
char *versionNumberF = "0.4";
long long verificationCnt = 0;
long long mappingCnt = 0;
long long mappedSeqCnt = 0;
long long completedSeqCnt = 0;
char *mappingOutput;
char *_msf_refGen = NULL;
int _msf_refGenLength = 0;
int _msf_refGenOffset = 0;
char *_msf_refGenName = NULL;
int _msf_refGenBeg;
int _msf_refGenEnd;
IHashTable *_msf_hashTable = NULL;
int *_msf_samplingLocs;
int *_msf_samplingLocsEnds;
int _msf_samplingLocsSize;
Read *_msf_seqList;
int _msf_seqListSize;
Pair *_msf_sort_seqList = NULL;
int *_msf_map_sort_seqList;
ReadIndexTable *_msf_rIndex = NULL;
int _msf_rIndexSize;
int _msf_rIndexMax;
SAM _msf_output;
OPT_FIELDS *_msf_optionalFields;
char *_msf_op;
int *_msf_verifiedLocs = NULL;
char _msf_numbers[200][3];
char _msf_cigar[5];
// READ SLICE
int _msf_totalSeqListSize;
MappingInfo *_msf_mappingInfo;
int *_msf_seqHits;
int _msf_openFiles = 0;
int _msf_maxLSize = 0;
int _msf_maxRSize = 0;
BestFullMappingInfo *bestHitMappingInfo;
int _msf_maxFile = 0;
char _msf_fileName[4000][200][2][FILE_NAME_LENGTH];
int _msf_fileCount[4000];
char *_msf_readHasConcordantMapping;
int *_msf_oeaMapping;
int *_msf_discordantMapping;
void freeAllMapping();
void initBestMapping(int totalReadNumber) {
int i = 0;
bestHitMappingInfo = getMem(totalReadNumber * sizeof(BestFullMappingInfo));
for (i = 0; i < totalReadNumber; i++) {
bestHitMappingInfo[i].loc = -1;
bestHitMappingInfo[i].tprob = 0.0;
}
}
void finalizeBestSingleMapping()
{
int i = 0;
char *_tmpQual, *_tmpSeq;
char rqual[SEQ_LENGTH + 1];
rqual[SEQ_LENGTH] = '\0';
for(i = 0; i < _msf_seqListSize; i++) {
if(_msf_seqList[i].hits[0] != 0) {
if (bestHitMappingInfo[i].dir) {
reverse(_msf_seqList[i].qual, rqual, SEQ_LENGTH);
_tmpQual = rqual;
_tmpSeq = _msf_seqList[i].rseq;
}
else {
_tmpQual = _msf_seqList[i].qual;
_tmpSeq = _msf_seqList[i].seq;
}
_msf_output.QNAME = _msf_seqList[i].name;
_msf_output.FLAG = 16 * bestHitMappingInfo[i].dir;
_msf_output.RNAME = bestHitMappingInfo[i].chr;
_msf_output.POS = bestHitMappingInfo[i].loc;
_msf_output.MAPQ = mapQ(i);
_msf_output.CIGAR = bestHitMappingInfo[i].cigar;
_msf_output.MRNAME = "*";
_msf_output.MPOS = 0;
_msf_output.ISIZE = 0;
_msf_output.SEQ = _tmpSeq;
_msf_output.QUAL = _tmpQual;
_msf_output.optSize = 2;
_msf_output.optFields = _msf_optionalFields;
_msf_optionalFields[0].tag = "NM";
_msf_optionalFields[0].type = 'i';
_msf_optionalFields[0].iVal = bestHitMappingInfo[i].err;
_msf_optionalFields[1].tag = "MD";
_msf_optionalFields[1].type = 'Z';
_msf_optionalFields[1].sVal = bestHitMappingInfo[i].md;
output(_msf_output);
}
}
freeMem(bestHitMappingInfo, _msf_seqListSize * sizeof(FullMappingInfo));
}
int compare(const void *a, const void *b) {
return ((Pair *) a)->hv - ((Pair *) b)->hv;
}
void preProcessReads() {
int i = 0;
//printf("reads=%d\n", _msf_seqListSize);
_msf_sort_seqList = getMem(_msf_seqListSize * sizeof(Pair));
for (i = 0; i < _msf_seqListSize; i++) {
_msf_sort_seqList[i].hv = hashVal(_msf_seqList[i].seq);
_msf_sort_seqList[i].readNumber = i;
//printf("%d", _msf_sort_seqList[i].readNumber);
}
qsort(_msf_sort_seqList, _msf_seqListSize, sizeof(Pair), compare);
_msf_map_sort_seqList = getMem(_msf_seqListSize * sizeof(int));
for (i = 0; i < _msf_seqListSize; i++)
_msf_map_sort_seqList[_msf_seqList[i].readNumber] = i;
}
void initFAST(Read *seqList, int seqListSize, int *samplingLocs,
int samplingLocsSize, char *genFileName) {
int i;
if (_msf_optionalFields == NULL) {
_msf_op = getMem(SEQ_LENGTH);
if (pairedEndMode) {
_msf_optionalFields = getMem(8 * sizeof(OPT_FIELDS));
} else {
_msf_optionalFields = getMem(2 * sizeof(OPT_FIELDS));
}
for (i = 0; i < 200; i++) {
sprintf(_msf_numbers[i], "%d%c", i, '\0');
}
sprintf(_msf_cigar, "%dM", SEQ_LENGTH);
}
if (_msf_samplingLocsEnds == NULL) {
_msf_samplingLocs = samplingLocs;
_msf_samplingLocsSize = samplingLocsSize;
_msf_samplingLocsEnds = getMem(sizeof(int) * _msf_samplingLocsSize);
for (i = 0; i < _msf_samplingLocsSize; i++) {
_msf_samplingLocsEnds[i] = _msf_samplingLocs[i] + WINDOW_SIZE - 1;
}
_msf_seqList = seqList;
_msf_seqListSize = seqListSize;
preProcessReads();
_msf_oeaMapping = getMem(_msf_seqListSize * sizeof(int));
for (i = 0; i < _msf_seqListSize; i++) {
_msf_oeaMapping[i] = 0;
}
_msf_discordantMapping = getMem(_msf_seqListSize * sizeof(int));
for (i = 0; i < _msf_seqListSize; i++) {
_msf_discordantMapping[i] = 0;
}
}
if (_msf_refGenName == NULL) {
_msf_refGenName = getMem(4 * SEQ_LENGTH);
}
_msf_refGen = getRefGenome();
_msf_refGenLength = strlen(_msf_refGen);
_msf_refGenOffset = getRefGenomeOffset();
snprintf(_msf_refGenName, 4 * SEQ_LENGTH, "%s%c", getRefGenomeName(), '\0');
_msf_refGenName[strlen(getRefGenomeName())] = '\0';
if (_msf_verifiedLocs != NULL) {
freeMem(_msf_verifiedLocs, sizeof(int) * (_msf_refGenLength + 1));
}
_msf_verifiedLocs = (int *) getMem(sizeof(int) * (_msf_refGenLength + 1));
for (i = 0; i <= _msf_refGenLength; i++)
_msf_verifiedLocs[i] = _msf_seqListSize * 10 + 1;
if (pairedEndMode && _msf_seqHits == NULL) {
_msf_mappingInfo = getMem(seqListSize * sizeof(MappingInfo));
for (i = 0; i < seqListSize; i++) {
_msf_mappingInfo[i].next = NULL;
_msf_mappingInfo[i].size = 0;
}
_msf_seqHits = getMem((_msf_seqListSize) * sizeof(int));
for (i = 0; i < _msf_seqListSize; i++) {
_msf_seqHits[i] = 0;
}
_msf_readHasConcordantMapping = getMem(
_msf_seqListSize / 2 * sizeof(char));
for (i = 0; i < _msf_seqListSize / 2; i++) {
_msf_readHasConcordantMapping[i] = 0;
}
initLoadingRefGenome(genFileName);
}
if (_msf_refGenOffset == 0) {
_msf_refGenBeg = 1;
} else {
_msf_refGenBeg = CONTIG_OVERLAP - SEQ_LENGTH + 2 + errThreshold;
}
_msf_refGenEnd = _msf_refGenLength - SEQ_LENGTH + 1;
}
void finalizeFAST() {
freeMem(_msf_seqHits, (_msf_seqListSize) * sizeof(int));
freeMem(_msf_refGenName, 4 * SEQ_LENGTH);
//freeMem(_msf_map_sort_seqList, sizeof(Pair) * _msf_seqListSize);
//freeMem(_msf_sort_seqList, sizeof(int) * _msf_seqListSize);
}
int addCigarSize(int cnt) {
if (cnt < 10)
return 1;
else if (cnt < 100)
return 2;
return 3;
}
// Generate Cigar from the back tracking matrix
void generateCigar(char *matrix, int matrixLength, char *cigar) {
int i = 0;
int counterM = 0;
int counterI = 0;
int counterD = 0;
int cigarSize = 0;
cigar[0] = '\0';
while (i < matrixLength) {
if (matrix[i] == 'M') {
counterM++;
if (counterI != 0) {
sprintf(cigar, "%s%dI", cigar, counterI);
cigarSize += addCigarSize(counterI) + 1;
cigar[cigarSize] = '\0';
counterI = 0;
} else if (counterD != 0) {
sprintf(cigar, "%s%dD", cigar, counterD);
cigarSize += addCigarSize(counterD) + 1;
cigar[cigarSize] = '\0';
counterD = 0;
}
} else if (matrix[i] == 'I') {
if (counterM != 0) {
sprintf(cigar, "%s%dM", cigar, counterM);
cigarSize += addCigarSize(counterM) + 1;
cigar[cigarSize] = '\0';
counterM = 0;
} else if (counterD != 0) {
sprintf(cigar, "%s%dD", cigar, counterD);
cigarSize += addCigarSize(counterD) + 1;
cigar[cigarSize] = '\0';
counterD = 0;
}
counterI++;
i++;
} else if (matrix[i] == 'D') {
if (counterM != 0) {
sprintf(cigar, "%s%dM", cigar, counterM);
cigarSize += addCigarSize(counterM) + 1;
cigar[cigarSize] = '\0';
counterM = 0;
} else if (counterI != 0) {
sprintf(cigar, "%s%dI", cigar, counterI);
cigarSize += addCigarSize(counterI) + 1;
cigar[cigarSize] = '\0';
counterI = 0;
}
counterD++;
i++;
} else {
counterM++;
if (counterI != 0) {
sprintf(cigar, "%s%dI", cigar, counterI);
cigarSize += addCigarSize(counterI) + 1;
cigar[cigarSize] = '\0';
counterI = 0;
} else if (counterD != 0) {
sprintf(cigar, "%s%dD", cigar, counterD);
cigarSize += addCigarSize(counterD) + 1;
cigar[cigarSize] = '\0';
counterD = 0;
}
}
i++;
}
if (counterM != 0) {
sprintf(cigar, "%s%dM", cigar, counterM);
cigarSize += addCigarSize(counterM) + 1;
cigar[cigarSize] = '\0';
counterM = 0;
} else if (counterI != 0) {
sprintf(cigar, "%s%dI", cigar, counterI);
cigarSize += addCigarSize(counterI) + 1;
cigar[cigarSize] = '\0';
counterI = 0;
} else if (counterD != 0) {
sprintf(cigar, "%s%dD", cigar, counterD);
cigarSize += addCigarSize(counterD) + 1;
cigar[cigarSize] = '\0';
counterD = 0;
}
cigar[cigarSize] = '\0';
}
// Creates the Cigar output from the mismatching positions format [0-9]+(([ACTGN]|\^[ACTGN]+)[0-9]+)*
void generateCigarFromMD(char *mismatch, int mismatchLength, char *cigar) {
int i = 0;
int j = 0;
int start = 0;
int cigarSize = 0;
cigar[0] = '\0';
while (i < mismatchLength) {
if (mismatch[i] >= '0' && mismatch[i] <= '9') {
start = i;
while (mismatch[i] >= '0' && mismatch[i] <= '9'
&& i < mismatchLength)
i++;
int value = atoi(mismatch + start);
for (j = 0; j < value - 1; j++) {
cigar[cigarSize] = 'M';
cigarSize++;
}
cigar[cigarSize] = 'M';
} else if (mismatch[i] == '^') {
cigar[cigarSize] = 'I';
i++;
} else if (mismatch[i] == '\'') {
cigar[cigarSize] = 'D';
i++;
} else {
cigar[cigarSize] = 'M';
cigarSize++;
}
cigarSize++;
i++;
}
cigar[cigarSize] = '\0';
}
void generateSNPSAM(char *matrix, int matrixLength, char *outputSNP) {
int i = 0;
int counterM = 0;
int counterD = 0;
char delete[100];
int snpSize = 0;
outputSNP[0] = '\0';
delete[0] = '\0';
while (i < matrixLength) {
if (matrix[i] == 'M') {
counterM++;
if (counterD != 0) {
delete[counterD] = '\0';
counterD = 0;
sprintf(outputSNP, "%s^%s", outputSNP, delete);
snpSize += strlen(delete) + 1;
outputSNP[snpSize] = '\0';
delete[0] = '\0';
}
} else if (matrix[i] == 'D') {
if (counterM != 0) {
sprintf(outputSNP, "%s%d", outputSNP, counterM);
snpSize += addCigarSize(counterM);
outputSNP[snpSize] = '\0';
counterM = 0;
delete[counterD] = matrix[i + 1];
i++;
counterD++;
} else if (counterD != 0) {
delete[counterD] = matrix[i + 1];
counterD++;
i++;
} else {
delete[counterD] = matrix[i + 1];
counterD++;
i++;
}
} else if (matrix[i] == 'I') {
if (counterM != 0) {
// sprintf(outputSNP, "%s%d\0", outputSNP, counterM);
//counterM++;
} else if (counterD != 0) {
delete[counterD] = '\0';
sprintf(outputSNP, "%s^%s", outputSNP, delete);
snpSize += strlen(delete) + 1;
outputSNP[snpSize] = '\0';
counterD = 0;
delete[0] = '\0';
}
i++;
} else {
if (counterM != 0) {
sprintf(outputSNP, "%s%d", outputSNP, counterM);
snpSize += addCigarSize(counterM);
outputSNP[snpSize] = '\0';
counterM = 0;
}
if (counterD != 0) {
delete[counterD] = '\0';
counterD = 0;
sprintf(outputSNP, "%s^%s", outputSNP, delete);
snpSize += strlen(delete) + 1;
outputSNP[snpSize] = '\0';
delete[0] = '\0';
}
sprintf(outputSNP, "%s%c", outputSNP, matrix[i]);
snpSize += 1;
outputSNP[snpSize] = '\0';
}
i++;
}
if (counterM != 0) {
sprintf(outputSNP, "%s%d", outputSNP, counterM);
snpSize += addCigarSize(counterM);
outputSNP[snpSize] = '\0';
counterM = 0;
} else if (counterD != 0) {
delete[counterD] = '\0';
sprintf(outputSNP, "%s^%s", outputSNP, delete);
snpSize += strlen(delete) + 1;
outputSNP[snpSize] = '\0';
counterD = 0;
}
outputSNP[snpSize] = '\0';
}
int compareEntrySize(const void *a, const void *b) {
return ((*(key_struct*) a).key_entry_size
- (*(key_struct*) b).key_entry_size);
}
int compareOut(const void *a, const void *b) {
FullMappingInfo *aInfo = (FullMappingInfo *) a;
FullMappingInfo *bInfo = (FullMappingInfo *) b;
return aInfo->loc - bInfo->loc;
}
void outputPairFullMappingInfo(FILE *fp, int readNumber) {
char *seq1, *seq2, *rseq1, *rseq2, *qual1, *qual2;
char rqual1[SEQ_LENGTH + 1], rqual2[SEQ_LENGTH + 1];
rqual1[SEQ_LENGTH] = rqual2[SEQ_LENGTH] = '\0';
seq1 = _msf_seqList[readNumber * 2].seq;
rseq1 = _msf_seqList[readNumber * 2].rseq;
qual1 = _msf_seqList[readNumber * 2].qual;
reverse(_msf_seqList[readNumber * 2].qual, rqual1, SEQ_LENGTH);
seq2 = _msf_seqList[readNumber * 2 + 1].seq;
rseq2 = _msf_seqList[readNumber * 2 + 1].rseq;
qual2 = _msf_seqList[readNumber * 2 + 1].qual;
reverse(_msf_seqList[readNumber * 2 + 1].qual, rqual2, SEQ_LENGTH);
if (bestHitMappingInfo[readNumber * 2].loc == -1
&& bestHitMappingInfo[readNumber * 2 + 1].loc == -1)
return;
else {
char *seq;
char *qual;
char d1;
char d2;
int isize;
int proper = 0;
// ISIZE CALCULATION
// The distance between outer edges
isize = abs(
bestHitMappingInfo[readNumber * 2].loc
- bestHitMappingInfo[readNumber * 2 + 1].loc)
+ SEQ_LENGTH - 2;
if (bestHitMappingInfo[readNumber * 2].loc
- bestHitMappingInfo[readNumber * 2 + 1].loc > 0) {
isize *= -1;
}
d1 = (bestHitMappingInfo[readNumber * 2].dir == -1) ? 1 : 0;
d2 = (bestHitMappingInfo[readNumber * 2 + 1].dir == -1) ? 1 : 0;
if (d1) {
seq = rseq1;
qual = rqual1;
} else {
seq = seq1;
qual = qual1;
}
//TODO for CG like SOLID
if ( (d1 && d2) || (!d1 && !d2)) {
proper = 2;
} else {
proper = 0;
}
_msf_output.POS = bestHitMappingInfo[readNumber * 2].loc;
_msf_output.MPOS = bestHitMappingInfo[readNumber * 2 + 1].loc;
_msf_output.FLAG = 1 + proper + 16 * d1 + 32 * d2 + 64;
_msf_output.ISIZE = isize;
_msf_output.SEQ = seq;
_msf_output.QUAL = qual;
_msf_output.QNAME = _msf_seqList[readNumber * 2].name;
_msf_output.RNAME = bestHitMappingInfo[readNumber * 2].chr;
_msf_output.MAPQ = mapQ(readNumber * 2) + mapQ(readNumber * 2 + 1);
_msf_output.CIGAR = bestHitMappingInfo[readNumber * 2].cigar;
_msf_output.MRNAME = "=";
_msf_output.optSize = 2;
_msf_output.optFields = _msf_optionalFields;
_msf_optionalFields[0].tag = "NM";
_msf_optionalFields[0].type = 'i';
_msf_optionalFields[0].iVal = bestHitMappingInfo[readNumber * 2].err;
_msf_optionalFields[1].tag = "MD";
_msf_optionalFields[1].type = 'Z';
_msf_optionalFields[1].sVal = bestHitMappingInfo[readNumber * 2].md;
output(_msf_output);
if (d2) {
seq = rseq2;
qual = rqual2;
} else {
seq = seq2;
qual = qual2;
}
_msf_output.POS = bestHitMappingInfo[readNumber * 2 + 1].loc;
_msf_output.MPOS = bestHitMappingInfo[readNumber * 2].loc;
_msf_output.FLAG = 1 + proper + 16 * d2 + 32 * d1 + 128;
_msf_output.ISIZE = -isize;
_msf_output.SEQ = seq;
_msf_output.QUAL = qual;
_msf_output.QNAME = _msf_seqList[readNumber * 2].name;
_msf_output.RNAME = bestHitMappingInfo[readNumber * 2].chr;
_msf_output.MAPQ = mapQ(readNumber * 2) + mapQ(readNumber * 2 + 1);
_msf_output.CIGAR = bestHitMappingInfo[readNumber * 2 + 1].cigar;
_msf_output.MRNAME = "=";
_msf_output.optSize = 2;
_msf_output.optFields = _msf_optionalFields;
_msf_optionalFields[0].tag = "NM";
_msf_optionalFields[0].type = 'i';
_msf_optionalFields[0].iVal = bestHitMappingInfo[readNumber * 2 + 1].err;
_msf_optionalFields[1].tag = "MD";
_msf_optionalFields[1].type = 'Z';
_msf_optionalFields[1].sVal = bestHitMappingInfo[readNumber * 2 + 1].md;
output(_msf_output);
}
}
/*
Find the closet one to the c
@return 0: if the x1 is closer to c
1: if the x2 is closer to c
2: if both distance are equal
-1: if error
*/
int findNearest(int x1, int x2, int c) {
if (abs(x1 - c) < abs(x2 - c))
return 0;
else if (abs(x1 - c) > abs(x2 - c))
return 1;
else if (abs(x1 - c) == abs(x2 - c))
return 2;
else
return -1;
}
//void initBestMapping(int totalReadNumber) {
// bestHitMappingInfo = getMem(totalReadNumber * sizeof(BestFullMappingInfo));
//
// int i = 0;
// for (i = 0; i < totalReadNumber; i++) {
// bestHitMappingInfo[i].loc = -1;
// bestHitMappingInfo[i].tprob = 0.0;
// }
//}
void performBestMapping(int readCnt) {
int i = 0;
for (i = 0; i < readCnt / 2; i++)
outputPairFullMappingInfo(NULL, i);
}
void finalizeBestMapping(int readCnt) {
freeMem(bestHitMappingInfo, readCnt * sizeof(BestFullMappingInfo));
}
void finalizeBestConcordantDiscordant() {
int i = 0;
for (i = 0; i < _msf_seqListSize / 2; i++) {
outputPairFullMappingInfo(NULL, i);
}
freeMem(bestHitMappingInfo, _msf_seqListSize * sizeof(BestFullMappingInfo));
}
double mapProb(int readNumber, char *md, int dir, int err) {
int i = 0;
int mdlen = strlen(md);
char buf[MAX_CIGAR_SIZE];
int j = 0;
double phred = 0.0;
int errloc = 0;
int errcnt = 0; //since I cannot calculate deletion base quality
buf[0] = 0;
if (err == 0)
return 1.0;
while (i<mdlen){
if (isdigit(md[i])) buf[j++]=md[i++];
else if (isalpha(md[i])){
/* mismatch */
errcnt++;
buf[j] = '\0';
if (j != 0)
errloc += atoi(buf);
else if (i!=0)
errloc++;
j=0; buf[0]=0;
if (dir)
phred += (double) (_msf_seqList[readNumber].qual[SEQ_LENGTH-errloc-1] - 33);
else
phred += (double) (_msf_seqList[readNumber].qual[errloc] - 33);
i++;
}
else if (md[i]=='^'){
/* insertion to the read / deletion from reference */
if (j!=0){
buf[j]=0;
errloc += atoi(buf);
buf[0] = 0;
}
j=0;
i++; /* pass ^ */
while (isalpha(md[i++])) j++;
errloc += j;
j = 0;
}
}
double indel_prob = 1;
if (errcnt != err)
indel_prob = 0.0002 * (err - errcnt);
return pow(10, -1 * (phred / 10)) * indel_prob;
}
int mapQ(int readNumber) {
int mapqual;
double mapprob;
mapprob = mapProb(readNumber, bestHitMappingInfo[readNumber].md,
bestHitMappingInfo[readNumber].dir, bestHitMappingInfo[readNumber].err);
if (mapprob == bestHitMappingInfo[readNumber].tprob)
mapqual = 40;
else
mapqual = (int) (round(-10.0 * log10(1 - (mapprob / bestHitMappingInfo[readNumber].tprob))));
if (mapqual > 40) mapqual = 40;
return mapqual;
}
void setFullMappingInfo(int readNumber, int loc, int dir, int err, int score,
char *md, char * refName, char *cigar) {
bestHitMappingInfo[readNumber].loc = loc;
bestHitMappingInfo[readNumber].dir = dir;
bestHitMappingInfo[readNumber].err = err;
bestHitMappingInfo[readNumber].score = score;
strncpy(bestHitMappingInfo[readNumber].md, md, strlen(md) + 1);
strncpy(bestHitMappingInfo[readNumber].chr, refName, strlen(refName) + 1);
strncpy(bestHitMappingInfo[readNumber].cigar, cigar, strlen(cigar) + 1);
}
void setPairFullMappingInfo(int readNumber, FullMappingInfo mi1,
FullMappingInfo mi2) {
bestHitMappingInfo[readNumber * 2].loc = mi1.loc;
bestHitMappingInfo[readNumber * 2].dir = mi1.dir;
bestHitMappingInfo[readNumber * 2].err = mi1.err;
bestHitMappingInfo[readNumber * 2].score = mi1.score;
snprintf(bestHitMappingInfo[readNumber * 2].chr, MAX_REF_SIZE, "%s",
_msf_refGenName);
strncpy(bestHitMappingInfo[readNumber * 2].md, mi1.md, strlen(mi1.md) + 1);
strncpy(bestHitMappingInfo[readNumber * 2].cigar, mi1.cigar,
strlen(mi1.cigar) + 1);
bestHitMappingInfo[readNumber * 2 + 1].loc = mi2.loc;
bestHitMappingInfo[readNumber * 2 + 1].dir = mi2.dir;
bestHitMappingInfo[readNumber * 2 + 1].err = mi2.err;
bestHitMappingInfo[readNumber * 2 + 1].score = mi2.score;
snprintf(bestHitMappingInfo[readNumber * 2 + 1].chr, MAX_REF_SIZE, "%s",
_msf_refGenName);
strncpy(bestHitMappingInfo[readNumber * 2 + 1].md, mi2.md,
strlen(mi2.md) + 1);
strncpy(bestHitMappingInfo[readNumber * 2 + 1].cigar, mi2.cigar,
strlen(mi2.cigar) + 1);
}
int outputPairedEnd(int pre_unmappedCnt) {
int i = 0;
char cigar[MAX_CIGAR_SIZE];
int tmpOut;
FILE* in1[_msf_openFiles];
FILE* in2[_msf_openFiles];
char fname1[_msf_openFiles][FILE_NAME_LENGTH];
char fname2[_msf_openFiles][FILE_NAME_LENGTH];
FILE *out = NULL, *out1 = NULL;
char fname3[FILE_NAME_LENGTH];
char fname4[FILE_NAME_LENGTH];
int meanDistanceMapping = 0;
char rqual1[SEQ_LENGTH + 1];
char rqual2[SEQ_LENGTH + 1];
int tmp = 0;
loadRefGenome(&_msf_refGen, &_msf_refGenName, &tmpOut);
if (pairedEndDiscordantMode) {
sprintf(fname3, "%s__%s__disc", mappingOutputPath, mappingOutput);
sprintf(fname4, "%s__%s__oea", mappingOutputPath, mappingOutput);
out = fileOpen(fname3, "a");
out1 = fileOpen(fname4, "a");
}
FullMappingInfo *mi1 = getMem(sizeof(FullMappingInfo) * _msf_maxLSize);
FullMappingInfo *mi2 = getMem(sizeof(FullMappingInfo) * _msf_maxRSize);
_msf_fileCount[_msf_maxFile] = 0;
for (i = 0; i < _msf_openFiles; i++) {
sprintf(fname1[i], "%s__%s__%s__%d__1.tmp", mappingOutputPath,
_msf_refGenName, mappingOutput, i);
sprintf(_msf_fileName[_msf_maxFile][_msf_fileCount[_msf_maxFile]][0],
"%s", fname1[i]);
sprintf(fname2[i], "%s__%s__%s__%d__2.tmp", mappingOutputPath,
_msf_refGenName, mappingOutput, i);
sprintf(_msf_fileName[_msf_maxFile][_msf_fileCount[_msf_maxFile]][1],
"%s", fname2[i]);
in1[i] = fileOpen(fname1[i], "r");
in2[i] = fileOpen(fname2[i], "r");
_msf_fileCount[_msf_maxFile]++;
}
_msf_maxFile++;
int size;
int j, k;
int size1, size2;
meanDistanceMapping =
(pairedEndDiscordantMode == 1) ?
(minPairEndedDiscordantDistance
+ maxPairEndedDiscordantDistance) / 2 + SEQ_LENGTH :
(minPairEndedDistance + maxPairEndedDistance) / 2
+ SEQ_LENGTH;
for (i = 0; i < _msf_seqListSize / 2; i++) {
size1 = size2 = 0;
for (j = 0; j < _msf_openFiles; j++) {
tmpOut = fread(&size, sizeof(int), 1, in1[j]);
if (size > 0) {
for (k = 0; k < size; k++) {
mi1[size1 + k].dir = 1;
tmpOut = fread(&(mi1[size1 + k].loc), sizeof(int), 1, in1[j]);
tmpOut = fread(&(mi1[size1 + k].err), sizeof(int), 1, in1[j]);
tmpOut = fread(&(mi1[size1 + k].cigarSize), sizeof(int), 1, in1[j]);
tmpOut = fread((mi1[size1 + k].cigar), sizeof(char), mi1[size1 + k].cigarSize, in1[j]);
mi1[size1 + k].cigar[mi1[size1 + k].cigarSize] = '\0';
tmpOut = fread(&(mi1[size1 + k].mdSize), sizeof(int), 1, in1[j]);
tmpOut = fread((mi1[size1 + k].md), sizeof(char), (mi1[size1 + k].mdSize), in1[j]);
mi1[size1 + k].md[mi1[size1 + k].mdSize] = '\0';
if (mi1[size1 + k].loc < 1) {
mi1[size1 + k].loc *= -1;
mi1[size1 + k].dir = -1;
}
}
qsort(mi1 + size1, size, sizeof(FullMappingInfo), compareOut);
size1 += size;
}
}
for (j = 0; j < _msf_openFiles; j++) {
tmpOut = fread(&size, sizeof(int), 1, in2[j]);
if (size > 0) {
for (k = 0; k < size; k++) {
mi2[size2 + k].dir = 1;
tmpOut = fread(&(mi2[size2 + k].loc), sizeof(int), 1, in2[j]);
tmpOut = fread(&(mi2[size2 + k].err), sizeof(int), 1, in2[j]);
tmpOut = fread(&(mi2[size2 + k].cigarSize), sizeof(int), 1, in2[j]);
tmpOut = fread((mi2[size2 + k].cigar), sizeof(char), mi2[size2 + k].cigarSize, in2[j]);
mi2[size2 + k].cigar[mi2[size2 + k].cigarSize] = '\0';
tmpOut = fread(&(mi2[size2 + k].mdSize), sizeof(int), 1, in2[j]);
tmpOut = fread((mi2[size2 + k].md), sizeof(char), mi2[size2 + k].mdSize, in2[j]);
mi2[size2 + k].md[mi2[size2 + k].mdSize] = '\0';
if (mi2[size2 + k].loc < 1) {
mi2[size2 + k].loc *= -1;
mi2[size2 + k].dir = -1;
}
}
qsort(mi2 + size2, size, sizeof(FullMappingInfo), compareOut);
size2 += size;
}
}
int lm, ll, rl, rm;
int pos = 0;
if (pairedEndDiscordantMode) {
for (j = 0; j < size1; j++) {
lm = mi1[j].loc - maxPairEndedDiscordantDistance + 1;
ll = mi1[j].loc - minPairEndedDiscordantDistance + 1;
rl = mi1[j].loc + minPairEndedDiscordantDistance - 1;
rm = mi1[j].loc + maxPairEndedDiscordantDistance - 1;
while (pos < size2 && mi2[pos].loc < lm) {
pos++;
}
k = pos;
while (k < size2 && mi2[k].loc <= rm) {
if (mi2[k].loc <= ll || mi2[k].loc >= rl) {
if ( (mi1[j].dir == 1 && mi2[k].dir == 1)
|| (mi1[j].dir == -1 && mi2[k].dir == -1)) {
_msf_seqList[i * 2].hits[0] = 1;
_msf_seqList[i * 2 + 1].hits[0] = 1;
if (nosamMode != 0) {
size1 = 0;
size2 = 0;
}
break;
}
}
k++;
}
}
_msf_seqHits[i * 2] += size1;
_msf_seqHits[i * 2 + 1] += size2;
if (_msf_seqHits[i * 2 + 1] * _msf_seqHits[i * 2]
> DISCORDANT_CUT_OFF && nosamMode != 0) {
_msf_seqList[i * 2].hits[0] = 1;
_msf_seqList[i * 2 + 1].hits[0] = 1;
size1 = 0;
size2 = 0;
}
int rNo = 0;
int loc = 0;
int err = 0;
float sc = 0;
char l = 0;
//write the OEA data
if (_msf_seqHits[i * 2] == 0){
for (k = 0; k < size2 && _msf_oeaMapping[i * 2 + 1] < maxOEAOutput; k++) {
rNo = i * 2 + 1;
loc = mi2[k].loc * mi2[k].dir;
err = mi2[k].err;
sc = mi2[k].score;
l = strlen(_msf_refGenName);
tmp = fwrite(&rNo, sizeof(int), 1, out1);
tmp = fwrite(&l, sizeof(char), 1, out1);
tmp = fwrite(_msf_refGenName, sizeof(char), l, out1);
tmp = fwrite(&loc, sizeof(int), 1, out1);
tmp = fwrite(&err, sizeof(int), 1, out1);
tmp = fwrite(&sc, sizeof(float), 1, out1);
if (mi2[k].cigarSize > SEQ_LENGTH || mi2[k].cigarSize <= 0)
printf("ERROR CIGAR size=%d %s\n", mi2[k].cigarSize, _msf_seqList[i * 2 + 1].seq);
tmp = fwrite(&(mi2[k].cigarSize), sizeof(int), 1, out1);
tmp = fwrite((mi2[k].cigar), sizeof(char), mi2[k].cigarSize, out1);
tmp = fwrite(&(mi2[k].mdSize), sizeof(int), 1, out1);
//if (mi2[k].mdSize > SEQ_LENGTH || mi1[k].mdSize <= 0)
if (mi2[k].mdSize > SEQ_LENGTH || mi1[k].mdSize < 0)
printf("ERROR mdsize = %d %s\n", mi1[k].mdSize, _msf_seqList[i * 2].seq);
tmp = fwrite((mi2[k].md), sizeof(char), mi2[k].mdSize, out1);
_msf_oeaMapping[i * 2 + 1]++;
}
}
if (_msf_seqHits[i * 2 + 1] == 0){
for (j = 0; j < size1 && _msf_oeaMapping[i * 2] < maxOEAOutput; j++) {
rNo = i * 2;
loc = mi1[j].loc * mi1[j].dir;
err = mi1[j].err;
sc = mi1[j].score;
l = strlen(_msf_refGenName);