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sam.h
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sam.h
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#ifndef SAM_H
#define SAM_H
#include "constants.h"
#include "helper.h"
#include "parameters.h"
/**
* Stores a hit, and the number of corresponding identical sequences in the input files
*/
typedef struct {
char threadId; // one char ('A', 'B', etc.) per thread, written in the (unique) read name
count_t *readIds; // one read id for each output file, the id is given to the first read (in case of multiple reads per sequence)
char *readNames; // concatenated read names
count_t *counts;
unsigned int flag;
int rid;
uint64_t pos;
char cigar[MAX_CIGAR_SIZE];
char *sequence;
char *quality;
unsigned int nHits;
unsigned int hitId;
unsigned int nErrors;
} samLine_t;
void createSamLine (samLine_t *samLine, char threaId, count_t *readIds, count_t *counts, char *sequence, char *quality) {
samLine->threadId = threaId;
samLine->readIds = readIds;
samLine->counts = counts;
samLine->sequence = sequence;
samLine->quality = quality;
}
/*
void freeSamLine (samLine_t *samLine) {
free(samLine->counts);
free(samLine->sequence);
free(samLine->quality);
}
*/
int samLineComparator (const void *samLine1, const void *samLine2) {
int difference = ((samLine_t *) samLine1)->rid - ((samLine_t *) samLine2)->rid;
if (difference != 0) return difference;
return ((samLine_t *) samLine1)->pos - ((samLine_t *) samLine2)->pos;
}
unsigned int computeMapq (unsigned int nHits, unsigned int nErrors) {
if ((nHits > 1) || (nErrors >= 40)) {
return 0;
}
else {
return 40 - nErrors;
}
}
void swapSamLines (samLine_t *samLine1, samLine_t *samLine2) {
samLine_t tmp = *samLine1;
*samLine1 = *samLine2;
*samLine2 = tmp;
}
void printSamLine (const samLine_t *samLine) {
printf("%s (%p, %p) pos %i:%" PRId64 " %u/%u hits, counts:", samLine->sequence, samLine, samLine->sequence, samLine->rid, samLine->pos, samLine->hitId, samLine->nHits);
for (unsigned int i = 0; i < parameters->nReadsFiles; ++i) {
printf(" %u", samLine->counts[i]);
}
printf("\n");
}
/**
* Copy one SAM information to the buffer
*/
void copyToSamLine (samLine_t *samLine, size_t nCounts, count_t *readIds, count_t *counts, char *readNames, unsigned int flag, int rid, int64_t pos, bwtint_t nHits, bwtint_t hitId, unsigned int nErrors, const char *cigar, const char *sequence, const char *quality) {
memcpy(samLine->readIds, readIds, nCounts * sizeof(count_t));
samLine->readNames = readNames;
memcpy(samLine->counts, counts, nCounts * sizeof(count_t));
strcpy(samLine->cigar, cigar);
strcpy(samLine->sequence, sequence);
strcpy(samLine->quality, quality);
samLine->rid = rid;
samLine->flag = flag;
samLine->pos = pos;
samLine->nHits = nHits;
samLine->hitId = hitId;
samLine->nErrors = nErrors;
//printf("Adding sam line: ");
//printSamLine(samLine);
}
void printSamTailLine (FILE *file, samLine_t *samLine) {
fprintf(file, "\t%u\t%s\t%" PRId64 "\t%d\t%s\t*\t0\t0\t%s\t%s\tNH:i:%u\tHI:i:%u\tIH:i:%u\tNM:i:%u\n", samLine->flag, (samLine->rid == -1)? "*": bns->anns[samLine->rid].name, samLine->pos, computeMapq(samLine->nHits, samLine->nErrors), samLine->cigar, samLine->sequence, samLine->quality, samLine->nHits, samLine->hitId, samLine->nHits, samLine->nErrors);
}
void printSamLineUnique (FILE *file, samLine_t *samLine) {
fprintf(file, "read_%c_%u_x", samLine->threadId, samLine->readIds[0]);
for (size_t readsFileId = 0; readsFileId < parameters->nReadsFiles; ++readsFileId) {
fprintf(file, "_%" PRIu32, samLine->counts[readsFileId]);
}
printSamTailLine(file, samLine);
}
void printSamLineMultiple (FILE *file, samLine_t *samLine, unsigned int fileId) {
for (unsigned int countId = 0; countId < samLine->counts[fileId]; ++countId) {
size_t readNameLength = strlen(samLine->readNames);
fprintf(file, "%s", samLine->readNames);
samLine->readNames += readNameLength + 1;
printSamTailLine(file, samLine);
}
/*
for (unsigned int countId = 0; countId < samLine->counts[fileId]; ++countId) {
fprintf(file, "read_%c_%u", samLine->threadId, samLine->readIds[fileId] + countId);
printSamTailLine(file, samLine);
}
*/
}
/**
* This stores all the hits for one sequence (possibly in several files).
*/
typedef struct {
count_t *readIds;
char *readNames;
FILE **outputFiles;
count_t *counts;
unsigned int sequenceSize;
unsigned int backtraceSize;
char *backtraceCigar;
unsigned char *backtraceLengths;
char *forwardCigar;
char *backwardCigar;
char *forwardSeq;
char *backwardSeq;
char *forwardQual;
char *backwardQual;
bool isBackwardSet;
size_t maxSamLines;
pthread_mutex_t *writeMutex;
samLine_t *samLines;
count_t *samLinesReadIds;
count_t *samLinesCounts;
char *samLinesSequences;
char *samLinesQualities;
size_t nSamLines;
} outputSam_t;
void createOutputSam (outputSam_t *outputSam, unsigned int readSize, pthread_mutex_t *mutex, char threadId) {
count_t *samLinesReadIds;
count_t *samLinesCounts;
char *samLinesSequences;
char *samLinesQualities;
unsigned int readIdOffset = (parameters->uniqueOutputFile)? 1: parameters->nReadsFiles;
outputSam->maxSamLines = MAX(N_SAM_LINES, 2 * parameters->maxNHits);
outputSam->sequenceSize = readSize;
outputSam->isBackwardSet = false;
outputSam->readIds = (count_t *) callocOrDie(parameters->nReadsFiles, sizeof(count_t));
outputSam->counts = (count_t *) mallocOrDie(parameters->nReadsFiles * sizeof(count_t));
outputSam->backtraceCigar = (char *) mallocOrDie(MAX_CIGAR_SIZE * sizeof(char));
outputSam->backtraceLengths = (unsigned char *) mallocOrDie(MAX_CIGAR_SIZE * sizeof(unsigned char));
outputSam->forwardCigar = (char *) mallocOrDie(MAX_CIGAR_SIZE * sizeof(char));
outputSam->backwardCigar = (char *) mallocOrDie(MAX_CIGAR_SIZE * sizeof(char));
outputSam->forwardSeq = (char *) mallocOrDie((readSize+1) * sizeof(char));
outputSam->backwardSeq = (char *) mallocOrDie((readSize+1) * sizeof(char));
outputSam->forwardQual = (char *) mallocOrDie((readSize+1) * sizeof(char));
outputSam->backwardQual = (char *) mallocOrDie((readSize+1) * sizeof(char));
outputSam->samLinesReadIds = (count_t *) mallocOrDie(outputSam->maxSamLines * readIdOffset * sizeof(count_t));
outputSam->samLinesCounts = (count_t *) mallocOrDie(outputSam->maxSamLines * parameters->nReadsFiles * sizeof(count_t));
outputSam->samLinesSequences = (char *) mallocOrDie(outputSam->maxSamLines * (readSize+1) * sizeof(char));
outputSam->samLinesQualities = (char *) mallocOrDie(outputSam->maxSamLines * (readSize+1) * sizeof(char));
outputSam->writeMutex = mutex;
outputSam->nSamLines = 0;
outputSam->samLines = (samLine_t *) mallocOrDie(outputSam->maxSamLines * sizeof(samLine_t));
samLinesReadIds = outputSam->samLinesReadIds;
samLinesCounts = outputSam->samLinesCounts;
samLinesSequences = outputSam->samLinesSequences;
samLinesQualities = outputSam->samLinesQualities;
for (size_t samLineId = 0; samLineId < outputSam->maxSamLines; ++samLineId) {
createSamLine(&outputSam->samLines[samLineId], threadId, samLinesReadIds, samLinesCounts, samLinesSequences, samLinesQualities);
samLinesReadIds += readIdOffset;
samLinesCounts += parameters->nReadsFiles;
samLinesSequences += readSize+1;
samLinesQualities += readSize+1;
}
}
void freeOutputSam (outputSam_t *outputSam) {
free(outputSam->readIds);
free(outputSam->counts);
free(outputSam->backtraceCigar);
free(outputSam->backtraceLengths);
free(outputSam->forwardCigar);
free(outputSam->backwardCigar);
free(outputSam->forwardSeq);
free(outputSam->backwardSeq);
free(outputSam->forwardQual);
free(outputSam->backwardQual);
free(outputSam->samLinesReadIds);
free(outputSam->samLinesCounts);
free(outputSam->samLinesSequences);
free(outputSam->samLinesQualities);
free(outputSam->samLines);
}
/**
* Create CIGAR string from the backtrace
*/
void computeCigar (outputSam_t *outputSam) {
size_t forwardCigarSize = 0;
size_t backwardCigarSize = 0;
//TODO Optimize this
forwardCigarSize = backwardCigarSize = 0;
for (size_t backtraceId = 0; backtraceId < outputSam->backtraceSize; ++backtraceId) {
forwardCigarSize += sprintf(outputSam->forwardCigar+forwardCigarSize, "%i%c", outputSam->backtraceLengths[backtraceId], outputSam->backtraceCigar[backtraceId]);
backwardCigarSize += sprintf(outputSam->backwardCigar+backwardCigarSize, "%i%c", outputSam->backtraceLengths[outputSam->backtraceSize-backtraceId-1], outputSam->backtraceCigar[outputSam->backtraceSize-backtraceId-1]);
}
outputSam->forwardCigar[forwardCigarSize] = 0;
outputSam->backwardCigar[backwardCigarSize] = 0;
}
void setCigarNoError (outputSam_t *outputSam, unsigned int readLength) {
sprintf(outputSam->forwardCigar, "%u=", readLength);
sprintf(outputSam->backwardCigar, "%u=", readLength);
}
/**
* Compute the reverse-complement of the sequence and the quality
*/
void computeReverseComplement (outputSam_t *outputSam) {
size_t readLength = strlen(outputSam->forwardSeq);
outputSam->isBackwardSet = true;
reverseComplementSequence(outputSam->forwardSeq, outputSam->backwardSeq, readLength);
reverseSequence(outputSam->forwardQual, outputSam->backwardQual, readLength);
}
/**
* Print all the SAM buffers to the output file
*/
void writeToSam (outputSam_t *outputSam, bool compulsory) {
if ((! compulsory) && (outputSam->nSamLines < outputSam->maxSamLines / 2)) {
return;
}
if (pthread_mutex_lock(outputSam->writeMutex) != 0) {
fprintf(stderr, "Error, Cannot acquire write mutex!\nExiting.\n");
exit(EXIT_FAILURE);
}
if (parameters->uniqueOutputFile) {
for (unsigned int samLineId = 0; samLineId < outputSam->nSamLines; ++samLineId) {
printSamLineUnique(outputSam->outputFiles[0], &outputSam->samLines[samLineId]);
}
}
else {
for (unsigned int samLineId = 0; samLineId < outputSam->nSamLines; ++samLineId) {
for (unsigned int fileId = 0; fileId < parameters->nReadsFiles; ++fileId) {
//printf("printing output: ");
//printSamLine(&outputSam->samLines[samLineId]);
printSamLineMultiple(outputSam->outputFiles[fileId], &outputSam->samLines[samLineId], fileId);
}
}
}
if (pthread_mutex_unlock(outputSam->writeMutex) != 0) {
fprintf(stderr, "Error, Cannot release write mutex!\nExiting.\n");
exit(EXIT_FAILURE);
}
outputSam->nSamLines = 0;
}
/**
* Remove near exact hits
*/
void removeDuplicatesOutputLines(outputSam_t *outputSam, size_t nLines) {
assert(nLines <= outputSam->nSamLines);
size_t samLineOffset = outputSam->nSamLines - nLines;
size_t nNewLines = 1;
samLine_t *samLineFirst = outputSam->samLines + samLineOffset;
samLine_t *samLineFree = samLineFirst + 1;
samLine_t *samLineCurrent = samLineFree;
int previousRid, currentRid;
uint64_t previousPos, currentPos;
unsigned int previousStrand, currentStrand;
if (nLines <= 1) {
return;
}
/*
printf("Reducing\n");
for (unsigned int i = 0; i < nLines; ++i) {
printSamLine(&outputSam->samLines[samLineOffset+i]);
}
*/
qsort(samLineFirst, nLines, sizeof(samLine_t), samLineComparator);
previousRid = samLineFirst->rid;
previousPos = samLineFirst->pos;
previousStrand = samLineFirst->flag & CIGAR_REVERSE;
/*
printf("Sorting\n");
for (unsigned int i = 0; i < nLines; ++i) {
printSamLine(&outputSam->samLines[samLineOffset+i]);
}
*/
for (unsigned int samLineId = 1; samLineId < nLines; ++samLineId, ++samLineCurrent) {
/*
printf("Step: previousRid: %i, previousPos: %" PRId64 ", current: %p, free: %p\n", previousRid, previousPos, samLineCurrent, samLineFree);
for (unsigned int i = 0; i < nNewLines; ++i) {
printSamLine(&outputSam->samLines[samLineOffset+i]);
}
*/
currentRid = samLineCurrent->rid;
currentPos = samLineCurrent->pos;
currentStrand = samLineCurrent->flag & CIGAR_REVERSE;
if ((previousRid != currentRid) || (currentPos - previousPos > samLineCurrent->nErrors) || (previousStrand != currentStrand)) {
if (samLineFree != samLineCurrent) {
//memcpy(samLineFree, samLineCurrent, sizeof(samLine_t));
swapSamLines(samLineFree, samLineCurrent);
}
++samLineFree;
++nNewLines;
previousRid = currentRid;
previousPos = currentPos;
previousStrand = currentStrand;
}
}
if (nNewLines != nLines) {
outputSam->samLines[samLineOffset].flag = outputSam->samLines[samLineOffset].flag & (~ CIGAR_SECONDARY_HIT);
for (unsigned int hitId = 0; hitId < nNewLines; ++hitId) {
outputSam->samLines[samLineOffset+hitId].hitId = hitId + 1;
outputSam->samLines[samLineOffset+hitId].nHits = nNewLines;
}
}
/*
printf(" to:\n");
for (unsigned int i = 0; i < nNewLines; ++i) {
printSamLine(&outputSam->samLines[samLineOffset+i]);
}
*/
outputSam->nSamLines = samLineOffset + nNewLines;
writeToSam(outputSam, false);
}
/**
* Add a new SAM information to the buffer
*/
void addSamLine (outputSam_t *outputSam, unsigned int flag, int rid, int64_t pos, bwtint_t nHits, bwtint_t hitId, unsigned int nErrors, const char *cigar, const char *sequence, const char *quality) {
assert(outputSam->nSamLines < outputSam->maxSamLines);
for (unsigned int fileId = 0; fileId < parameters->nOutputFileNames; ++fileId) {
size_t readNamesOffset = 0;
copyToSamLine(&outputSam->samLines[outputSam->nSamLines], parameters->nReadsFiles, outputSam->readIds, outputSam->counts, outputSam->readNames + readNamesOffset, flag, rid, pos, nHits, hitId, nErrors, cigar, sequence, quality);
for (count_t i = 0; i < outputSam->counts[fileId]; ++i) {
readNamesOffset += strlen(outputSam->readNames) + 1;
}
}
++outputSam->nSamLines;
}
/**
* Add one SAM info (too many hits) to the buffer
*/
void printReadLineManyHits (char *seq, char *qual, bwtint_t nHits, unsigned int nErrors, outputSam_t *outputSam) {
addSamLine(outputSam, 4, -1, 0, nHits, 0, nErrors, "*", seq, qual);
writeToSam(outputSam, false);
for (unsigned int fileId = 0; fileId < parameters->nOutputFileNames; ++fileId) {
outputSam->readIds[fileId] += outputSam->counts[fileId];
}
}
/**
* Decide whether to use the direct or the reverse-complement before add one SAM info to the buffer
*/
void printReadLine (bool forward, unsigned int flag, int rid, int64_t pos, bwtint_t nHits, bwtint_t hitId, unsigned int nErrors, outputSam_t *outputSam) {
char *cigar, *seq, *qual;
if (! outputSam->isBackwardSet) {
computeReverseComplement(outputSam);
}
if (forward) {
cigar = outputSam->forwardCigar;
seq = outputSam->forwardSeq;
qual = outputSam->forwardQual;
}
else {
cigar = outputSam->backwardCigar;
seq = outputSam->backwardSeq;
qual = outputSam->backwardQual;
}
addSamLine(outputSam, flag, rid, pos, nHits, hitId, nErrors, cigar, seq, qual);
}
/**
* Print a read, which maps only once, and with no error
*/
void printReadUniqueNoError (int strand, int rid, int64_t pos, size_t readLength, outputSam_t *outputSam) {
unsigned int flag = 0;
setCigarNoError(outputSam, readLength);
if (strand == 0) {
flag = CIGAR_REVERSE;
}
printReadLine(strand != 0, flag, rid, pos, 1, 1, 0, outputSam);
//fprintf(outputSamFile, "%s\t%u\t%s\t%" PRId64 "\t40\t%zuM\t*\t0\t0\t%s\t%s\tNH:i:1\tHI:i:1\tIH:i:1\tNM:i:0\n", qname, flag, chrName, pos, readLength, seq, qual);
writeToSam(outputSam, false);
}
/**
* Collect information before printing read
*/
void preparePrintRead (uint64_t pos, int rid, int strand, bwtint_t nHits, bwtint_t hitId, unsigned int nErrors, outputSam_t *outputSam) {
unsigned int flag = (hitId == 1)? 0: CIGAR_SECONDARY_HIT;
if (strand == 0) {
flag |= CIGAR_REVERSE;
}
printReadLine(strand != 0, flag, rid, pos, nHits, hitId, nErrors, outputSam);
}
void setCountsSam (outputSam_t *outputSam, count_t *counts) {
memcpy(outputSam->counts, counts, parameters->nReadsFiles * sizeof(count_t));
}
void updateReadIds (outputSam_t *outputSam) {
if (parameters->uniqueOutputFile) {
++outputSam->readIds[0];
return;
}
for (unsigned int fileId = 0; fileId < parameters->nOutputFileNames; ++fileId) {
outputSam->readIds[fileId] += outputSam->counts[fileId];
}
}
void openSamFiles (FILE **outputFiles) {
for (unsigned int fileId = 0; fileId < parameters->nOutputFileNames; ++fileId) {
outputFiles[fileId] = fopen(parameters->outputSamFileNames[fileId], "w");
if (outputFiles[fileId] == NULL) {
fprintf(stderr, "Error, cannot open output file '%s' for writing!\nExiting.\n", parameters->outputSamFileNames[fileId]);
exit(EXIT_FAILURE);
}
fprintf(outputFiles[fileId], "@HD\tVN:1.6\tSO:unsorted\n");
for (int i = 0; i < bns->n_seqs; ++i) {
fprintf(outputFiles[fileId], "@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
}
}
}
void closeSamFiles (FILE **outputFiles) {
for (unsigned int fileId = 0; fileId < parameters->nOutputFileNames; ++fileId) {
fclose(outputFiles[fileId]);
}
}
#endif