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|
#include "ReadsMapping.h"
#include "MappingResult.h"
const int MISQUERYCHECKPOINT = 100000;
int parallelMappingLongReads(vector<string>& readSetsList,\
CGenome_Index_TableQ& indexTable, MappingOpts P)
{
P.clearOutputFileName(readSetsList.size() > 1);
indexTable.bExcludeAmbiguous = P.bExcludeAmbiguousReads;
//__OPENMP_FOR_PARALLEL__(#pragma)
int i;
#ifdef _OPENMP
int numberOfCPUs = omp_get_num_procs();
LOG_INFO("\nInfo %d: %d CPUs detected. %s.\n",\
INFO_LOG, numberOfCPUs, BLANK_LINE);
#pragma omp parallel for
#endif
for (i = 0; i < (int)readSetsList.size(); i++) {
CReadsMapping mapping(P);
const char* readSetName = (readSetsList.at(i)).c_str();
if (checkFileExist(readSetName)) {
CLongReadsSet longReadSet(readSetName, P.readsFileFormat, P.readLength,\
P.allowedNumOfNinRead, P.truncatedReadPrefix);
if (P.bIgnoreQS) {
longReadSet.ignoreQScores();
}
TIME_INFO(mapping.mapLongReads(longReadSet, indexTable), "Mapping takes");
}
}
return(0);
}
// Given a read set list and the index table, this function maps reads in parallel
int parallelMapping(vector<string>& readSetsList, \
CGenome_Index_TableQ& indexTable, MappingOpts P)
{
P.clearOutputFileName(readSetsList.size() > 1);
//__OPENMP_FOR_PARALLEL__(#pragma)
int i;
#ifdef _OPENMP
int numberOfCPUs = omp_get_num_procs();
LOG_INFO("\nInfo %d: %d CPUs detected. %s.\n",\
INFO_LOG, numberOfCPUs, BLANK_LINE);
#pragma omp parallel for
#endif
for (i = 0; i < (int)readSetsList.size(); i++) {
CReadInBitsSet readSet
(readSetsList.at(i).c_str(), \
P.readsFileFormat, P.truncatedReadPrefix,\
indexTable.uiRead_Length, P.allowedNumOfNinRead);
if (P.bIgnoreQS) {
readSet.ignoreQScores();
}
CReadsMapping mapping(P);
TIME_INFO(mapping.mapReads(readSet, indexTable), "Mapping completed");
}
return(0);
}
CReadsMapping::CReadsMapping(void)
{
this->initialization();
}
CReadsMapping::CReadsMapping(MappingOpts P)
{
this->initialization();
this->opt= P;
this->iMultiMappedLocationThreshold = P.maxAlignPerRead;
alignmentsQ[0].iMaxCapacity = P.maxAlignPerRead + 1; // store one more record
alignmentsQ[1].iMaxCapacity = P.maxAlignPerRead + 1; // So the load can be used to judge if overflow
if (P.bGetAllAlignments) {
// WARNING if index indexTable.bExcludeAmbiguous will have some error
alignmentsQ[0].setQueue_All_Best_OneFlag('A');
alignmentsQ[1].setQueue_All_Best_OneFlag('A');
}
if (P.outputFormat[0] != '\0') {
if (strcmp(P.outputFormat, "SAM") == 0 ||
strcmp(P.outputFormat, "sam") == 0 ) {
this->cOutputFormat = 's';
} else if (strcmp(P.outputFormat, "MAPPING") == 0 ||
strcmp(P.outputFormat, "mapping") == 0 ) {
this->cOutputFormat = 'm';
} else if (strcmp(P.outputFormat, "FASTQ") == 0 ||
strcmp(P.outputFormat, "fastq") == 0 ) {
this->cOutputFormat = 'F';
this->opt.bPrintFirstAlignmentOnly = true;
} else {
LOG_INFO("Info %d: Specified output format %s is not recognizable.\n", WARNING_LOG, P.outputFormat);
}
}
// check if the director exist, if not, create one
if (P.outputDir[0] != '\0') {
if (dirExist(P.outputDir) || createdir(P.outputDir) == 0) {
#ifdef WIN32
sprintf(this->opt.outputDir, "%s\\", P.outputDir);
#else
sprintf(this->opt.outputDir, "%s/", P.outputDir);
#endif
} else {
LOG_INFO("Info %d: Can't create dir %s.\n", WARNING_LOG, P.outputDir);
this->opt.outputDir[0] = '\0';
}
}
}
CReadsMapping::~CReadsMapping(void)
{
delete AlignResult;
delete MissReads;
}
void CReadsMapping::initialization(void)
{
this->AlignResult = NULL;
this->AmbiguousReads = NULL;
this->MissReads = NULL;
this->BadReads = NULL;
this->cOutputFormat = 'm';
}
int CReadsMapping::mapReadsSets(const char* ReadsSetsList, CGenome_Index_TableQ& table, bool bDiscardReadsWN)
{
// Counter for coverage is not initialize
this->initializeStatsCounter();
char readsFile[FILENAME_MAX];
ifstream readsFileList(ReadsSetsList);
while (GetNextFilenameFromListFile(readsFileList, readsFile)) {
CReadInBitsSet readSet(readsFile, this->opt.readsFileFormat,\
this->opt.truncatedReadPrefix,\
table.uiRead_Length, bDiscardReadsWN);
this->mapReads(readSet, table);
}
return(0);
}
int CReadsMapping::mapReads(CReadInBitsSet& readSet, const CGenome_Index_TableQ& table)
{
if (wrongIndex(readSet, table)) return(0);
unsigned qsShift = table.bMapReadInColors ? Phred_SCALE_QUAL_SHIFT : SolexaScoreEncodingShift;
getReadsFileFormat(readSet.InputFile, opt.readsFileFormat);
string seedStr = seedSymbol(table.chosenSeedId);
unsigned int uiReadLength = readSet.uiRead_Length;
printf("Mapping %s (%u-bp reads) with %s seed.%s\n", \
readSet.InputFile, uiReadLength, seedStr.c_str(), BLANK_LINE);
// if there are multiple gene in first chromosome.
// bool bPrintGeneName = (table.pgenomeNT->paChromosomes[0]->geneVec.table.size() >= 0);
this->initializeStatsCounter();
if (this->setUpIO4Aligment(readSet.InputFile, table) != 0) {
LOG_INFO("\nInfo %d: Fail to setup I/O files.", ERROR_LOG);
return(1);
}
readSet.setBadReadOutputFile(this->BadReads);
CAlignmentsQ& aQue = this->alignmentsQ[0];
while (readSet.get_next_capacity_reads(BUFFERED_READS_SIZE, opt.readtag_delimiter) != 0) {
vector<CReadInBits>::iterator it = readSet.pReadsSet->begin();
for (int i = 0; it != readSet.pReadsSet->end(); i++, it++) {
this->printCheckPointInfo(i);
readSet.get_read_id(i, aQue.tag);
aQue.read = *it;
aQue.qualityScores = readSet.getQScoresPtr(i);
bool map2forwardStrand = !opt.bMap2ReverseStrandOnly;
bool map2reverseStrand = !opt.bMap2ForwardStrandOnly;
if (table.bMapReadInColors) {
if(map2forwardStrand) {
bool clearQ;
table.queryReadColors(*it, aQue, clearQ = true, true);
}
if(map2reverseStrand) {
bool clearQ = this->opt.bMap2ReverseStrandOnly ? true : false;
table.queryReadColors(*it, aQue, clearQ, false);
}
} else {
bool clearQ;
if(map2forwardStrand) {
table.queryReadBases(*it, aQue, clearQ = true, true);
}
if(map2reverseStrand) {
clearQ = opt.bMap2ReverseStrandOnly ? true : false;
table.queryReadBases(*it, aQue, clearQ, false);
}
}
// statistics and output
if (aQue.load > 0) {
bookKeepMapping(aQue);
bool bPrintAlignment = this->printAlignmentOrNot(aQue, this->opt.bExcludeAmbiguousReads, this->opt.bPrintAmbiguousReadsOnly);
if (bPrintAlignment) {
this->dealMappedRead(table, aQue);
}
} else if (this->opt.bPrintUnMappedReads) {
char qs[MAX_READ_LENGTH];
qs[0] = '\0';
if (readSet.pQualScores != NULL) {
const char* qsPtr = readSet.pQualScores->qScores((unsigned int)i);
trQScores(table.uiRead_Length, qsShift, qsPtr, qs);
}
dealMissedRead(table.bMapReadInColors, aQue.tag, aQue.read, qs);
}
}
iReadCounter += (unsigned int)readSet.pReadsSet->size();
}
this->tearDownIO4Aligment();
this->iBadReadCounter = readSet.uiNo_of_Bad_Reads;
this->printMappingStats(cout, readSet.InputFile, opt.subDiffThreshold);
return(0);
}
// Map a single long read in two CReadInBits format
int CReadsMapping::queryALongReadInBase(CReadInBits& r1stHalf, CReadInBits& r2ndHalf, const CGenome_Index_TableQ& table, CAlignmentsQ& aQue) const
{
// TODO: The reads should be query and "Check" immediately before que.
// In this way, "short cut and filter can be applied right away. Should be changed
/*
table.queryReadBases(r1stHalf, aQue, true, true);
table.queryReadBases(r1stHalf, aQue, false, false);
table.extendAlignment(aQue, r2ndHalf);
aQue.filterAlignments(this->opt.subDiffThreshold, this->opt.bGetAllAlignments);
*/
const bool bOddReadLength = this->opt.bOddReadLengthAndLongRead;
const bool bAmbiguousOnly = this->opt.bPrintAmbiguousReadsOnly;
const bool bShortCutAE = this->opt.bExcludeAmbiguousReads && aQue.qAllInThreshold() && !bAmbiguousOnly;
const bool bShortCutE = this->opt.bExcludeAmbiguousReads && !bAmbiguousOnly;
const bool bShortCutB = !this->opt.bExcludeAmbiguousReads && !aQue.qAllInThreshold() && !bAmbiguousOnly;
const bool bMap2ForwardStrand = ! this->opt.bMap2ReverseStrandOnly;
const bool bMap2ReverseStrand = ! this->opt.bMap2ForwardStrandOnly;
if(bMap2ForwardStrand) {
bool clearQ;
table.queryLongReadBases(r1stHalf, r2ndHalf, bOddReadLength, aQue, 1, clearQ = true, true);
if (aQue.load > 1) {
if (bShortCutAE || (bShortCutE && aQue.MinDiff == 0)) {
return (aQue.load);
}
}
if (!(bShortCutB && aQue.MinDiff == 0)) {
table.queryLongReadBases(r1stHalf, r2ndHalf, bOddReadLength, aQue, 2, clearQ = false, true);
if (aQue.load > 1) {
if (bShortCutAE || (bShortCutE && aQue.MinDiff == 0)) {
return (aQue.load);
}
}
}
}
if(bMap2ReverseStrand) {
bool clearQ = this->opt.bMap2ReverseStrandOnly ? true : false;
table.queryLongReadBases(r1stHalf, r2ndHalf, bOddReadLength, aQue, 1, clearQ, false);
if (aQue.load > 1) {
if (bShortCutAE || (bShortCutE && aQue.MinDiff == 0)) {
return (aQue.load);
}
}
if (!(bShortCutB && aQue.MinDiff == 0)) {
table.queryLongReadBases(r1stHalf, r2ndHalf, bOddReadLength, aQue, 2, clearQ = false, false);
}
}
return(aQue.load);
}
int CReadsMapping::queryALongReadInColors(CReadInBits& r1stHalf, CReadInBits& r2ndHalf, const CGenome_Index_TableQ& table, CAlignmentsQ& aQue) const
{
LOG_INFO("\nInfo %d: Currently PerM doesn't support mapping SOLiD reads longer than 64 base pairs.\n",\
ERROR_LOG);
const bool bOddReadLength = this->opt.bOddReadLengthAndLongRead;
const bool bAmbiguousOnly = this->opt.bPrintAmbiguousReadsOnly;
const bool bShortCutAE = this->opt.bExcludeAmbiguousReads && aQue.qAllInThreshold() && !bAmbiguousOnly;
const bool bShortCutE = this->opt.bExcludeAmbiguousReads && !bAmbiguousOnly;
const bool bShortCutB = !this->opt.bExcludeAmbiguousReads && !aQue.qAllInThreshold() && !bAmbiguousOnly;
const bool bMap2ForwardStrand = ! this->opt.bMap2ReverseStrandOnly;
const bool bMap2ReverseStrand = ! this->opt.bMap2ForwardStrandOnly;
if(bMap2ForwardStrand) {
bool clearQ;
table.queryLongReadColors(r1stHalf, r2ndHalf, bOddReadLength, aQue, 1, clearQ = true, true);
if (aQue.load > 1) {
if (bShortCutAE || (bShortCutE && aQue.MinDiff == 0)) {
return (aQue.load);
}
}
if ( !(bShortCutB && aQue.MinDiff == 0)) {
table.queryLongReadColors(r1stHalf, r2ndHalf, bOddReadLength, aQue, 2, clearQ = false, true);
if (aQue.load > 1) {
if (bShortCutAE || (bShortCutE && aQue.MinDiff == 0)) {
return (aQue.load);
}
}
}
}
if(bMap2ReverseStrand) {
bool clearQ = this->opt.bMap2ReverseStrandOnly ? true : false;
table.queryLongReadColors(r1stHalf, r2ndHalf, bOddReadLength, aQue, 1, clearQ, false);
if (aQue.load > 1) {
if (bShortCutAE || (bShortCutE && aQue.MinDiff == 0)) {
return (aQue.load);
}
}
if ( !(bShortCutB && aQue.MinDiff == 0)) {
table.queryLongReadColors(r1stHalf, r2ndHalf, bOddReadLength, aQue, 2, clearQ = false, false);
}
}
return(aQue.load);
}
int CReadsMapping::printLogFile(const char* inputFile)
{
ofstream logFile(opt.logFileN, ofstream::app);
if (logFile.good()) {
this->printCommand(logFile, opt.fullCommand);
this->printMappingStats(logFile, inputFile, opt.subDiffThreshold);
this->printCommand(cout, opt.fullCommand);
this->printMappingStats(cout, inputFile, opt.subDiffThreshold);
} else {
this->printCommand(cout, opt.fullCommand);
this->printMappingStats(cout, inputFile, opt.subDiffThreshold);
}
logFile.close();
return(0);
}
// To map reads longer than MAX_READ_LENGTH, locate alignments using first half and check the mismatches in the second half
int CReadsMapping::mapLongReads(CLongReadsSet& longReadSet, const CGenome_Index_TableQ& table)
{
unsigned int uiReadLength = this->opt.readLength;
CAlignmentsQ& aQue = this->alignmentsQ[0];
CReadInBitsSet& readSet1stHalf = *(longReadSet.F_Reads);
CReadInBitsSet& readSet2ndHalf = *(longReadSet.R_Reads);
const char* readSetName = readSet1stHalf.InputFile;
// Flag that set the alignment is ambiguous or not
getReadsFileFormat(readSetName, opt.readsFileFormat);
string seedStr = seedSymbol(table.chosenSeedId);
printf("Mapping %s (%u-bp reads) with %s seed.\n", \
readSetName, uiReadLength, seedStr.c_str());
this->initializeStatsCounter();
if (this->setUpIO4Aligment(readSetName, table) != 0) {
LOG_INFO("\nInfo %d: Fail to setup I/O files.", ERROR_LOG);
return(1);
}
longReadSet.setBadReadOutputFile(this->BadReads);
// alignmentsQ[0].setQueue_All_Best_OneFlag('A');
const bool bMapReadInColors = table.bMapReadInColors;
while (longReadSet.get_next_capacity_long_reads() > 0) {
int bufferedReadNo = this->checkPairedReadSetSize(readSet1stHalf, readSet2ndHalf);
vector<CReadInBits>::iterator it1, it2;
it1 = readSet1stHalf.pReadsSet->begin();
it2 = readSet2ndHalf.pReadsSet->begin();
for (int i = 0; i < bufferedReadNo; i++, it1++, it2++) {
this->printCheckPointInfo(i);
CMappingResult m;
if (bMapReadInColors) {
this->getLongColorReadInfo(readSet1stHalf, readSet2ndHalf, i, *it1, *it2, m);
this->queryALongReadInColors(*it1, *it2, table, aQue);
return(-1);
} else {
this->getLongBaseReadInfo(readSet1stHalf, readSet2ndHalf, i, *it1, *it2, m);
this->queryALongReadInBase(*it1, *it2, table, aQue);
}
// statistics and output
if (aQue.load > 0) {
bookKeepMapping(aQue);
bool bPrintAlignment = this->printAlignmentOrNot(aQue, this->opt.bExcludeAmbiguousReads, this->opt.bPrintAmbiguousReadsOnly);
if (bPrintAlignment) {
this->dealMappedLongRead(table, aQue, m);
}
} else if (this->opt.bPrintUnMappedReads) {
dealMissedRead(m);
}
}
this->iReadCounter += bufferedReadNo;
}
this->tearDownIO4Aligment();
this->iBadReadCounter = longReadSet.uiNo_of_Bad_Reads;
this->printLogFile(readSetName);
return(0);
}
int CReadsMapping::dealMissedRead(bool bMapReadInColors, const char* readName, CReadInBits r, const char* qs)
{
this->printRead(this->MissReads, bMapReadInColors, readName, r, qs);
return(this->iMissReadCounter++);
}
int CReadsMapping::dealAmbiguousRead(bool bMapReadInColors, const char* readName, CReadInBits r, const char* qs)
{
this->printRead(this->AmbiguousReads, bMapReadInColors, readName, r, qs);
return(this->iReadsMapped2tooManyLocations);
}
inline void CReadsMapping::printRead(FileOutputBuffer* FileBuf, bool bMapReadInColors, const char* readName, CReadInBits r, const char* qs)
{
char caRead[MAX_READ_LENGTH + 1];
if (bMapReadInColors) {
decodeColorReadWithPrimer(caRead, r);
} else {
r.decode(caRead);
}
if (qs == NULL || qs[0] == '\0') {
sprintf(FileBuf->caBufp, ">%s\n%s\n", readName, caRead);
} else {
sprintf(FileBuf->caBufp, "@%s\n%s\n+\n%s\n", readName, caRead, qs);
}
FileBuf->UpdateSize();
}
inline void CReadsMapping::printRead(FileOutputBuffer* FileBuf, CMappingResult& m)
{
const char* readSeqOrColors;
if (m.caRead[0] != '\0') {
readSeqOrColors = m.caRead;
} else {
readSeqOrColors = m.TAG;
}
if (m.QScores[0] == '\0') {
sprintf(FileBuf->caBufp, ">%s\n%s\n", m.QNAME, readSeqOrColors);
FileBuf->UpdateSize();
} else {
sprintf(FileBuf->caBufp, "@%s\n%s\n+\n%s\n", m.QNAME, readSeqOrColors, m.QScores);
FileBuf->UpdateSize();
}
}
int CReadsMapping::dealMissedRead(CMappingResult& m)
{
printRead(this->MissReads, m);
return(this->iMissReadCounter++);
}
int CReadsMapping::dealAmbiguousRead(CMappingResult& m)
{
printRead(this->AmbiguousReads, m);
return(this->iReadsMapped2tooManyLocations);
}
unsigned int CReadsMapping::checkPairedReadSetSize\
(CReadInBitsSet& firstHalfSet, CReadInBitsSet& SecondHalfSet)
{
unsigned int size1 = (unsigned int)firstHalfSet.pReadsSet->size();
unsigned int size2 = (unsigned int)SecondHalfSet.pReadsSet->size();
if (size1 == size2) {
return(size1);
} else {
LOG_INFO("Info %d: Not every read has the second half\n", WARNING_LOG);
return(min(size1, size2));
}
}
void printSingleEndReads(char format, unsigned int uiReadLength);
// This function print out alignments for each read and the corresponding information.
int CReadsMapping::dealMappedRead(const CGenome_Index_TableQ& table, CAlignmentsQ& aQue)
{
bool samFormat = (this->cOutputFormat == 's');
CMappingResult m(aQue, opt.readLength);
if (!table.bMapReadInColors) {
// TODO: get read
getReadQscores4Solexa(aQue, m, samFormat);
}
if (this->opt.bPrintAlignments) {
if (aQue.load < aQue.iMaxCapacity || this->opt.bPrintAmbiguousReadsOnly) {
for (unsigned int i = 0; i < aQue.load && i < aQue.iMaxCapacity; i++) {
getSingleMappingInfo(table, aQue, i, m, samFormat);
this->printSingleEndReads(m);
if (this->opt.bPrintFirstAlignmentOnly) {
break;
}
}
}
if (aQue.load >= aQue.iMaxCapacity) {
// If a read is mapped to over threshold place, don't print it
this->iReadsMapped2tooManyLocations++;
if (this->opt.bPrintAmbigReadsSeparately) {
this->dealAmbiguousRead(table.bMapReadInColors,aQue.tag, aQue.read, aQue.qualityScores);
/* The alternative ambiguous print will not include the adapter
const bool IF_COLOR2BASE = false;
const int FIRST_INDEX = 0;
getSingleMappingInfo(table, aQue, FIRST_INDEX, m, IF_COLOR2BASE);
this->dealAmbiguousRead(m);
*/
} else if (this->opt.bPrintAmbigReadsInOneLine) {
getSingleMappingInfo(table, aQue, 0, m, samFormat);
this->printSingleEndReads(m);
}
}
}
return(aQue.load);
}
int CReadsMapping::dealMappedLongRead\
(const CGenome_Index_TableQ& table, CAlignmentsQ& aQue, CMappingResult& m)
{
bool samFormat = (this->cOutputFormat == 's');
if (aQue.load < aQue.iMaxCapacity || this->opt.bPrintAmbiguousReadsOnly) {
if (this->opt.bPrintAlignments) {
for (unsigned int i = 0; i < aQue.load && i < aQue.iMaxCapacity; i++) {
// get and store all the output info in CMappingResult
getLongMappingInfo(table, aQue, samFormat, i, m); // TODO make change for SOLiD long read
this->printSingleEndReads(m);
if (this->opt.bPrintFirstAlignmentOnly) {
break;
}
}
}
}
if (aQue.load >= aQue.iMaxCapacity) {
// If a read is mapped to over threshold place, don't print it
this->iReadsMapped2tooManyLocations++;
if (this->opt.bPrintAmbigReadsSeparately) {
this->dealAmbiguousRead(m);
} else if (this->opt.bPrintAmbigReadsInOneLine) {
getLongMappingInfo(table, aQue, samFormat, 0, m);
this->printSingleEndReads(m);
}
}
return(aQue.load);
}
int CReadsMapping::printSingleEndReads(CMappingResult& m)
{
string dummyStr = "";
int map_score = 0;
switch (this->cOutputFormat) {
case 's':
printAMappingInSam(this->AlignResult, m);
break;
case 'F':
printAMappingInFastq(this->AlignResult, m);
break;
case 'g':
printAMappingInGff(this->AlignResult, m, map_score, dummyStr);
break;
default:
printAMappingInPerM(this->AlignResult, m, this->opt.bPrintNM);
break;
}
return(0);
}
/*
int CReadsMapping::printMappingsInBEDformat(FileOutputBuffer &OBuf, char* caKmer,
CMapOfSingleRead& mapPatternsSet, unsigned int ReadID)
{
const unsigned int SUB_LEVEL = 4;
const char* RGB[SUB_LEVEL];
RGB[0] = "0,0,0";
RGB[1] = "0,0,255";
RGB[2] = "0,255,0";
RGB[3] = "255,0,0";
unsigned int readLength = this->uiKmer_Length;
for(int i = 0; i < mapPatternsSet.size; i++)
{ // For each kind of pattern
set<CSingleMapping,Comp>* pSet = &(mapPatternsSet.mappingsSets[i]);
set<CSingleMapping,Comp>::iterator j;
// Print each occurrence of a same pattern
for(j = pSet->begin(); j != pSet->end(); j++) {
unsigned int chrom = j->chrId;
unsigned int chromStart = j->chrLocusId;
unsigned int chromEnd = chromStart + readLength;
int name = ReadID;
int score = 1;
if( score > 0) {
char strand = j->bReverse ? '-' : '+';
unsigned int subNum = diNtStrWildCardComp(mapPatternsSet.caPattern[i], caKmer, readLength);
const char* subRGB = (subNum > (SUB_LEVEL - 1)) ? RGB[subNum] : RGB[SUB_LEVEL - 1] ;
sprintf(OBuf.caBufp,"chr%u %u %u read%d %d %c %d %d %s %d %d 0\n",
chrom, chromStart, chromEnd, name, score, strand, chromStart, chromEnd,
subRGB, subNum, readLength);
OBuf.UpdateSize();
} else {
// bad read;
}
}
// delete each set if it has been report
mapPatternsSet.mappingsSets[i].clear();
}
return(mapPatternsSet.size);
} */
// This private function returns a string as the prefix of the output file name for mapping
string getOutputFileNamePrefix(const char* dir, const CGenome_Index_TableQ& table, MappingOpts& opt)
{
// The prefix contains 4 parts: (0) dir (1) ref file (2) ambiguous flag (3) mismatch threshold
char outputPrefixStr[MAX_PATH];
char excludeAmbiguous = opt.bExcludeAmbiguousReads ? 'E' : 'B';
if (opt.bGetAllAlignments) excludeAmbiguous = 'A';
sprintf(outputPrefixStr, "%s%s_%c_%u_%d",\
dir, table.caRefName, excludeAmbiguous, table.chosenSeedId, opt.subDiffThreshold);
return(string(outputPrefixStr));
}
bool isGalaxyOutputPath(const char* fileName)
{
return(hasTheExtName(fileName, ".dat"));
}
bool isSupportedExtName(const char* fileN)
{
if (hasTheExtName(fileN, ".fasta") ||
hasTheExtName(fileN, ".fastq") ||
hasTheExtName(fileN, ".fq") ||
hasTheExtName(fileN, ".csfq") ||
hasTheExtName(fileN, ".csfastq") ||
hasTheExtName(fileN, ".csfasta") ||
hasTheExtName(fileN, ".dat") ||
hasTheExtName(fileN, ".txt")) {
return(true);
}
return(false);
}
string rmSupportedExtName(const char* fileN)
{
char newFileN[FILENAME_MAX];
strcpy(newFileN, fileN);
if (isSupportedExtName(fileN)) {
for (int i = (int)strlen(newFileN); i > 0; i--) {
if (newFileN[i] == '.') {
newFileN[i] = '\0';
return(string(newFileN));
}
}
}
return(string(fileN));
}
// generate the unmapped FileN, if the original one is not null
void getAmbiguousFileN(char* ambiguousFileN, const char* readFileN, const char* readFormat,\
const char* refN, bool bQual = false)
{
string refNStr = rmSupportedExtName(refN);
string readFileNStr = rmSupportedExtName(readFileN);
if (strcmp(ambiguousFileN, "") == 0) { // make sure the readFormat is valid
if (strcmp(readFormat, "csfasta") == 0) {
if (bQual) {
sprintf(ambiguousFileN, "%s_ambig_%s.%s", readFileNStr.c_str(), refNStr.c_str(), "fastq");
} else {
sprintf(ambiguousFileN, "%s_ambig_%s", readFileNStr.c_str(), refNStr.c_str()); // Not sure csfasta or not
}
} else {
if (readFormat[0] == '\0') {
sprintf(ambiguousFileN, "%s_ambig_%s", readFileNStr.c_str(), refNStr.c_str());
} else {
sprintf(ambiguousFileN, "%s_ambig_%s.%s", readFileNStr.c_str(), refNStr.c_str(), readFormat);
}
}
}
}
// generate the unmapped FileN, if the original one is not null
void getUnmappedFileN(char* unmappedFileN, const char* readFileN, const char* readFormat,\
const char* refN, bool bQual = false)
{
string refNStr = rmSupportedExtName(refN);
string readFileNStr = rmSupportedExtName(readFileN);
if (strcmp(unmappedFileN, "") == 0) { // make sure the readFormat is valid
if (strcmp(readFormat, "csfasta") == 0) {
if (bQual) {
sprintf(unmappedFileN, "%s_miss_%s.%s", readFileNStr.c_str(), refNStr.c_str(), "fastq");
} else {
sprintf(unmappedFileN, "%s_miss_%s", readFileNStr.c_str(), refNStr.c_str()); // Not sure csfasta or not
}
} else {
if (readFormat[0] == '\0') {
sprintf(unmappedFileN, "%s_miss_%s", readFileNStr.c_str(), refNStr.c_str());
} else {
sprintf(unmappedFileN, "%s_miss_%s.%s", readFileNStr.c_str(), refNStr.c_str(), readFormat);
}
}
}
}
// generate the unmapped FileN, if the original one is not null
void getBadReadsFileN(char* badFileN, const char* readFileN, const char* readFormat,\
const char* refN, bool bQual = false)
{
string refNStr = rmSupportedExtName(refN);
string readFileNStr = rmSupportedExtName(readFileN);
if (strcmp(badFileN, "") == 0) { // make sure the readFormat is valid
if (strcmp(readFormat, "csfasta") == 0) {
if (bQual) {
sprintf(badFileN, "%s_bad.%s", readFileNStr.c_str(), "fastq");
} else {
sprintf(badFileN, "%s_bad", readFileNStr.c_str()); // Not sure csfasta or not
}
} else {
if (readFormat[0] == '\0') {
sprintf(badFileN, "%s_bad", readFileNStr.c_str());
} else {
sprintf(badFileN, "%s_bad.%s", readFileNStr.c_str(), readFormat);
}
}
}
}
string CReadsMapping::getMappingFileN(const char* caReadsSetName, const CGenome_Index_TableQ& table)
{
if (this->cOutputFormat == 'm') {
strcpy(opt.outputFormat, "mapping");
} else if (this->cOutputFormat == 's') {
strcpy(opt.outputFormat, "sam");
} else if (this->cOutputFormat == 'F') {
strcpy(opt.outputFormat, "fastq");
}
char outputPath[MAX_LINE];
if (this->opt.outputFileN[0] == '\0') { // No output file has been set
string outFileNPrefix = getOutputFileNamePrefix(this->opt.outputDir, table, opt);
string fileNameOfReadSet = getBasename(caReadsSetName);
const char* extN = opt.outputFormat;
if (string(extN) == "sam" || string(extN) == "mapping" || string(extN) == "fastq") {
sprintf(outputPath, "%s_%s.%s", outFileNPrefix.c_str(), fileNameOfReadSet.c_str(), extN);
} else {
if (extN[0] != '0') {
char msg[MAX_LINE];
sprintf(msg, "The specified output format %s is unrecognizable.\n", extN);
cout << msg;
// LOG_INFO("%s", WARNING_LOG, msg);
}
sprintf(outputPath, "%s_%s", outFileNPrefix.c_str(), fileNameOfReadSet.c_str());
}
} else {
sprintf(outputPath, "%s%s", this->opt.outputDir, this->opt.outputFileN);
}
return(string(outputPath));
}
int CReadsMapping::setUpIO4Aligment(const char* caReadsSetName, const CGenome_Index_TableQ& table)
{
if (this->opt.bGetAllAlignments) {
// Find all alignments with in threshold, instead of queuing
// only all best(with the fewest mismatches) alignments as default.
alignmentsQ[0].setQueue_All_Best_OneFlag('A');
alignmentsQ[1].setQueue_All_Best_OneFlag('A');
}
char outputPath[MAX_PATH];
strcpy(outputPath, this->getMappingFileN(caReadsSetName, table).c_str());
// (1)Initialize the I/O for output the alignments
if (this->opt.bPrintAlignments) {
if (this->AlignResult == NULL) {
ofstream* AlignResultFile = new ofstream(outputPath);
this->AlignResult =
new FileOutputBuffer(ALIGNMENT_RESULT_FILE_BUFFER_SIZE, AlignResultFile);
if (this->AlignResult == NULL) {
ERR;//check new FileOutputBuffer
return(1);
} else if (this->cOutputFormat == 's') {
if (this->opt.bPrintSamHeader) {
string RG = getSamRG(caReadsSetName, table.bMapReadInColors);
vector<CGene> refs = table.pgenomeNT->getRefNamesLengths();
string commandLineStr = this->opt.fullCommand;
printSamHeader(AlignResult, refs, RG.c_str(), commandLineStr.c_str());
}
}
}
}
// (2)Initialize the I/O for output the up-mapped reads.
if (this->opt.bPrintUnMappedReads) {
// Make sure opt.readsFileFormat has been set
const char* refN = table.pgenomeNT->refName;
getUnmappedFileN(opt.unmappedFileN, caReadsSetName, opt.readsFileFormat, refN);
/* // This line force the output to be the right ext name (fasta, csfasta or fastq)
if (!isGalaxyOutputPath(opt.unmappedFileN)) {
string extName = string(".").append(string(opt.readsFileFormat));
chExtName(opt.unmappedFileN, extName.c_str());
}*/
if (this->MissReads == NULL) {
ofstream* MissReadsFile = new ofstream(opt.unmappedFileN);
this->MissReads =
new FileOutputBuffer(ALIGNMENT_RESULT_FILE_BUFFER_SIZE, MissReadsFile);
if (this->MissReads == NULL) {
ERR; // check new FileOutputBuffer
return(1);
}
}
}
// (3) Initialize the I/O for output the ambiguous reads over the threshold
if (this->opt.bPrintAmbigReadsSeparately) {
// Make sure opt.readsFileFormat has been set
const char* refN = table.pgenomeNT->refName;
getAmbiguousFileN(opt.ambiguousReadFileN, caReadsSetName, opt.readsFileFormat, refN);
if (this->AmbiguousReads == NULL) {
ofstream* ambiguousReadsFile = new ofstream(opt.ambiguousReadFileN);
this->AmbiguousReads =
new FileOutputBuffer(ALIGNMENT_RESULT_FILE_BUFFER_SIZE, ambiguousReadsFile);
if (this->AmbiguousReads == NULL) {
ERR; // check new FileOutputBuffer
return(1);
}
}
}
// (4) Initialize the I/O for output the bad reads or reads shorter than expected
if (this->opt.bPrintBadReads) {
// Make sure opt.readsFileFormat has been set
const char* refN = table.pgenomeNT->refName;
getBadReadsFileN(opt.badReadFileN, caReadsSetName, opt.readsFileFormat, refN);
if (this->BadReads == NULL) {
ofstream* badReadsFile = new ofstream(opt.badReadFileN);
this->BadReads =
new FileOutputBuffer(ALIGNMENT_RESULT_FILE_BUFFER_SIZE, badReadsFile);
if (this->BadReads == NULL) {
ERR; // check new FileOutputBuffer
return(1);
}
}
}
return(0);
}
int CReadsMapping::tearDownIO4Aligment(void)
{
// close file, which has been opened before
if (this->opt.bPrintAlignments) {
// this->AlignResult->removeEndBlankLine();
delete this->AlignResult;
this->AlignResult = NULL;
}
if (this->opt.bPrintUnMappedReads) {
// this->MissReads->removeEndBlankLine();
delete this->MissReads;
this->MissReads = NULL;
}
if (this->opt.bPrintAmbigReadsSeparately) {
delete this->AmbiguousReads;
this->AmbiguousReads = NULL;
}
if (this->opt.bPrintBadReads) {
delete this->BadReads;
this->BadReads = NULL;
}
return(0);
}
void getSingleMappingSeq4Solexa(const CGenome_Index_TableQ& table, CMappingResult& m, bool noRef)
{
if (noRef) { // sam format doesn't need to know reference sequence
m.caRef[0] = '\0';
} else {
const unsigned int readLength = (unsigned int)strlen(m.caRead);
// (1) Get ref in bits
CReadInBits ref = table.pgenomeNTInBits->getSubstringInBits(m.uiGlobalMappedPos, readLength);
if (m.strand == '-') {
ref = reverseCompliment(readLength, ref);
}
// (2) Get ref seq
ref.decode(m.caRef);
}
}
void getQscores4Solexa(CAlignmentsQ& aQue, CMappingResult& m, bool samFormat)
{
if (aQue.qualityScores == NULL) {
m.mismatchScore = (int)m.uiDiff;
m.QScores[0] = '\0';
} else { // If quality score are available, get quality score
m.mismatchScore = alignmentScore(m.caRead, m.caRef, m.uiReadLength, aQue.qualityScores);
trQScores(m.uiReadLength, SolexaScoreEncodingShift, aQue.qualityScores, m.QScores);
if (samFormat) {
m.getReverseReadandQual();
}
}
}
void getReadQscores4Solexa(CAlignmentsQ& aQue, CMappingResult& m, bool samFormat)
{
aQue.read.decode(m.caRead);
getQscores4Solexa(aQue, m, samFormat);
}
inline CReadInBits getSingleMappingRef4SOLiD(const CGenome_Index_TableQ& table, CAlignmentsQ& aQue, CMappingResult& m, bool samFormat)
{
const unsigned int readlength = table.uiRead_Length;
// (1) Get ref in bits
CReadInBits ref = table.pgenomeNTInBits->getSubstringInBits(m.uiGlobalMappedPos, readlength);
if (m.strand == '-') {
ref = reverseCompliment(readlength, ref);
}
// (2) Get ref in color
CReadInBits colorsInRef = bases2Colors(ref);
m.SNPtype = returnSNPtype(aQue.read, colorsInRef);
// (3) Get ref in sequence
if(!samFormat) {
decodeColors(m.caRef, colorsInRef); // Show the reference for validation purpose
}
return(colorsInRef);
}
inline void getQualityScore4SOLiD(unsigned int readlength, CReadInBits &colorsInRef, CAlignmentsQ& aQue, CMappingResult& m, bool samFormat)
{
if (samFormat) { // correctRead
if (aQue.qualityScores == NULL) {
char dummyScore = (char)(20);
fillDummyQScores(readlength, dummyScore + Phred_SCALE_QUAL_SHIFT, m.QScores);
} else {
trQScores(readlength, Phred_SCALE_QUAL_SHIFT, aQue.qualityScores, m.QScores);
}
sprintf(m.TAG, "%s\tCS:Z:%s\tCQ:Z:%s", m.TAG, m.caRead, m.QScores);
//sprintf(m.TAG, "%s\tX1:Z:%s\tCS:Z:%s\tCQ:Z:%s", m.TAG, m.caRef, m.caRead, m.QScores);
correctAndDecodeRead(aQue.read, colorsInRef, samFormat, m.caRead, m.QScores);
if (m.strand == '-')
m.getReverseReadandQual();
} else {
if (aQue.qualityScores == NULL) {
m.mismatchScore = (int)m.uiDiff;
m.QScores[0] = '\0';
m.rawScores[0] = '\0';
} else {
m.mismatchScore = alignmentScore(m.caRead, m.caRef,\
readlength, aQue.qualityScores);
printCommaSepScoresStr(readlength, aQue.qualityScores, m.QScores);
}
}
}
void getSingleMappingSeqAndQ4SOLiD\
(const CGenome_Index_TableQ& table, CAlignmentsQ& aQue, CMappingResult& m, bool samFormat)
{
/*
const unsigned int readlength = table.uiRead_Length;
// (1) Get ref in bits
CReadInBits ref = table.pgenomeNTInBits->getSubstringInBits(m.uiGlobalMappedPos, readlength);
if (m.strand == '-') {
ref = reverseCompliment(readlength, ref);
}
// (2) Get ref (and read) in Seq
decodeColors(m.caRead, aQue.read);
CReadInBits colorsInRef = bases2Colors(ref);
*/
const unsigned int readlength = table.uiRead_Length;
// (1) Get read in Seq
decodeColors(m.caRead, aQue.read);
// (2) Get ref in Seq
CReadInBits colorsInRef = getSingleMappingRef4SOLiD(table, aQue, m, samFormat);
// (3) Get nucleotide and quality sequence
getQualityScore4SOLiD(readlength, colorsInRef, aQue, m, samFormat);
/*
if (samFormat) { // correctRead
if (aQue.qualityScores == NULL) {
char dummyScore = (char)(20);
fillDummyQScores(readlength, dummyScore + Phred_SCALE_QUAL_SHIFT, m.QScores);
} else {
trQScores(readlength, Phred_SCALE_QUAL_SHIFT, aQue.qualityScores, m.QScores);
}
sprintf(m.TAG, "%s\tCS:Z:%s\tCQ:Z:%s", m.TAG, m.caRead, m.QScores);
//sprintf(m.TAG, "%s\tX1:Z:%s\tCS:Z:%s\tCQ:Z:%s", m.TAG, m.caRef, m.caRead, m.QScores);
correctAndDecodeRead(aQue.read, colorsInRef, samFormat, m.caRead, m.QScores);
if (m.strand == '-')
m.getReverseReadandQual();
} else {
decodeColors(m.caRef, colorsInRef); // Show the reference for validation purpose
m.SNPtype = returnSNPtype(aQue.read, colorsInRef);
if (aQue.qualityScores == NULL) {
m.mismatchScore = (int)m.uiDiff;
m.QScores[0] = '\0';
m.rawScores[0] = '\0';
} else {
m.mismatchScore = alignmentScore(m.caRead, m.caRef,\
readlength, aQue.qualityScores);
printCommaSepScoresStr(readlength, aQue.qualityScores, m.QScores);
}
}*/
}
unsigned int getNoOfDiff(const char* str1, const char* str2, unsigned int readLength)
{
unsigned int noOfDiff = 0;
for (unsigned int i = 0; i < readLength; i++) {
if (str1[i] != str2[i]) {
noOfDiff ++;
}
}
return(noOfDiff);
}
// For one read to one location,
void getSingleMappingInfo(const CGenome_Index_TableQ& table, CAlignmentsQ& aQue,\
unsigned int mappingId, CMappingResult& m, bool samFormat)
{
getSingleMappingIndex(*(table.pgenomeNT), aQue, mappingId, m);
if (samFormat) { // must set after the strand flag is set
m.setSingleEndSamFields();
} // must set before the color seq and QUAL is set
if (table.bMapReadInColors) {
getSingleMappingSeqAndQ4SOLiD(table, aQue, m, samFormat);
} else {
getSingleMappingSeq4Solexa(table, m, samFormat);
}
if (aQue.qAllInThreshold() && !samFormat) {
int noMisMatch = getNoOfDiff(m.caRead, m.caRef, m.uiReadLength);
/* if(m.uiDiff != noMisMatch) {
ERR;
}*/
m.uiDiff = noMisMatch;
}
if (table.pbaRepeatRepresentativeFlag->b(aQue.aiHitIndex[mappingId])) {
m.MultipleMappedNo++;
}
}
void getLongMappingInfo(const CGenome_Index_TableQ& table, CAlignmentsQ& aQue, bool samFormat,\
unsigned int mappingId, CMappingResult& m)
{
// (1) Get index
getSingleMappingIndex(*(table.pgenomeNT), aQue, mappingId, m);
if (samFormat) {
m.setSingleEndSamFields();
} else {
// (2) Get Ref Sequence
getLongRefSeq(table, m, samFormat);
// (3) Get mismatch score
if (m.QScores[0] == '\0') {
m.mismatchScore = (int)m.uiDiff;
} else { // If quality score are available, get quality score
m.mismatchScore = alignmentScore(m.caRead, m.caRef, m.uiReadLength, m.rawScores);
}
if (m.strand == '-') {
reverseComplementKmer(m.caRef);
}
}
}
bool wrongIndex(const CReadInBitsSet& readSet, const CGenome_Index_TableQ& table)
{
if (readSet.uiRead_Length != table.uiRead_Length) {
LOG_INFO("Info %d: The index is not for read length %d, is for %d.\n",\
readSet.uiRead_Length, table.uiRead_Length, ERROR_LOG);
return(true);
}
bool bColorRead = (readSet.cFileType == 'Q' || readSet.cFileType == 'S');
if ( bColorRead != table.bMapReadInColors) {
if (bColorRead) {
LOG_INFO("Info %d: The index is not for color read.\n", ERROR_LOG);
} else {
LOG_INFO("Info %d: The index is for color read.\n", ERROR_LOG);
}
return(true);
}
return(false);
}
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