#include "blastalign.hpp"
#include "noalign.hpp"
#include "trimoligos.h"
+#include "oligos.h"
struct fastqRead {
vector<int> scores;
struct pairFastqRead {
fastqRead forward;
fastqRead reverse;
+ fastqRead findex;
+ fastqRead rindex;
pairFastqRead() {};
pairFastqRead(fastqRead f, fastqRead r) : forward(f), reverse(r){};
+ pairFastqRead(fastqRead f, fastqRead r, fastqRead fi, fastqRead ri) : forward(f), reverse(r), findex(fi), rindex(ri) {};
~pairFastqRead() {};
};
/**************************************************************************************************/
void help() { m->mothurOut(getHelpString()); }
private:
- bool abort, allFiles, trimOverlap, createFileGroup, createOligosGroup;
- string outputDir, ffastqfile, rfastqfile, align, oligosfile, rfastafile, ffastafile, rqualfile, fqualfile, file, format;
+ bool abort, allFiles, trimOverlap, createFileGroup, createOligosGroup, makeCount, noneOk, reorient;
+ string outputDir, ffastqfile, rfastqfile, align, oligosfile, rfastafile, ffastafile, rqualfile, fqualfile, findexfile, rindexfile, file, format, inputDir;
float match, misMatch, gapOpen, gapExtend;
- int processors, longestBase, insert, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs, deltaq;
+ int processors, longestBase, insert, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs, deltaq, numBarcodes, numFPrimers, numLinkers, numSpacers, numRPrimers;
vector<string> outputNames;
-
- map<int, oligosPair> barcodes;
- map<int, oligosPair> primers;
- vector<string> linker;
- vector<string> spacer;
- vector<string> primerNameVector;
- vector<string> barcodeNameVector;
+ Oligos* oligos;
vector<char> convertTable;
map<string, int> groupCounts;
fastqRead readFastq(ifstream&, bool&);
vector< vector< vector<string> > > preProcessData(unsigned long int&);
vector< vector<string> > readFileNames(string);
- vector< vector<string> > readFastqFiles(unsigned long int&, string, string);
+ vector< vector<string> > readFastqFiles(unsigned long int&, string, string, string, string);
vector< vector<string> > readFastaFiles(unsigned long int&, string, string);
//bool checkReads(fastqRead&, fastqRead&, string, string);
int createProcesses(vector< vector<string> >, string, string, string, vector<vector<string> >, int);
int driver(vector<string>, string, string, string, vector<vector<string> >, int, string);
- bool getOligos(vector<vector<string> >&, string);
- string reverseOligo(string);
- vector<pairFastqRead> getReads(bool ignoref, bool ignorer, fastqRead forward, fastqRead reverse, map<string, fastqRead>& uniques);
+ bool getOligos(vector<vector<string> >&, string, map<string, string>&);
+ vector<pairFastqRead> getReads(bool ignoref, bool ignorer, fastqRead forward, fastqRead reverse, map<string, fastqRead>& uniques, bool);
+ vector<pairFastqRead> mergeReads(vector<pairFastqRead> frReads, vector<pairFastqRead> friReads, map<string, pairFastqRead>& pairUniques);
};
/**************************************************************************************************/
string outputFasta;
string outputScrapFasta;
string outputMisMatches;
- string align, group;
+ string align, group, oligosfile;
vector<string> files;
vector<vector<string> > fastaFileNames;
MothurOut* m;
float match, misMatch, gapOpen, gapExtend;
int count, insert, threadID, pdiffs, bdiffs, tdiffs, deltaq;
- bool allFiles, createOligosGroup, createFileGroup, done, trimOverlap;
+ bool allFiles, createOligosGroup, createFileGroup, done, trimOverlap, reorient;
map<string, int> groupCounts;
map<string, string> groupMap;
- vector<string> primerNameVector;
- vector<string> barcodeNameVector;
- map<int, oligosPair> barcodes;
- map<int, oligosPair> primers;
+
contigsData(){}
- contigsData(string g, vector<string> f, string of, string osf, string om, string al, MothurOut* mout, float ma, float misMa, float gapO, float gapE, int thr, int delt, map<int, oligosPair> br, map<int, oligosPair> pr, vector<vector<string> > ffn, vector<string>bnv, vector<string> pnv, int pdf, int bdf, int tdf, bool cg, bool cfg, bool all, bool to, int tid) {
+ contigsData(string g, vector<string> f, string of, string osf, string om, string al, MothurOut* mout, float ma, float misMa, float gapO, float gapE, int thr, int delt, vector<vector<string> > ffn, string olig, bool ro, int pdf, int bdf, int tdf, bool cg, bool cfg, bool all, bool to, int tid) {
files = f;
outputFasta = of;
outputMisMatches = om;
count = 0;
outputScrapFasta = osf;
fastaFileNames = ffn;
- barcodes = br;
- primers = pr;
- barcodeNameVector = bnv;
- primerNameVector = pnv;
+ oligosfile = olig;
pdiffs = pdf;
bdiffs = bdf;
tdiffs = tdf;
createFileGroup = cfg;
threadID = tid;
deltaq = delt;
+ reorient = ro;
done=false;
}
};
string thisfqualfile = pDataArray->files[1];
string thisrfastafile = pDataArray->files[2];
string thisrqualfile = pDataArray->files[3];
+ string thisfindexfile = pDataArray->files[4];
+ string thisrindexfile = pDataArray->files[5];
- if (pDataArray->m->debug) { pDataArray->m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n"); }
+ if (pDataArray->m->debug) { pDataArray->m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n[DEBUG]: findex = " + thisfindexfile + ".\n[DEBUG]: rindex = " + thisrindexfile + ".\n"); }
if(pDataArray->allFiles){
for (int i = 0; i < pDataArray->fastaFileNames.size(); i++) { //clears old file
}
}
- ifstream inFFasta, inRFasta, inFQual, inRQual;
+ ifstream inFFasta, inRFasta, inFQual, inRQual, inFIndex, inRIndex;
ofstream outFasta, outMisMatch, outScrapFasta;
pDataArray->m->openInputFile(thisffastafile, inFFasta);
pDataArray->m->openInputFile(thisrfastafile, inRFasta);
pDataArray->m->openInputFile(thisfqualfile, inFQual);
pDataArray->m->openInputFile(thisrqualfile, inRQual);
}
+
+ if (thisfindexfile != "") { pDataArray->m->openInputFile(thisfindexfile, inFIndex); }
+ if (thisrindexfile != "") { pDataArray->m->openInputFile(thisrindexfile, inRIndex); }
+
pDataArray->m->openOutputFile(pDataArray->outputFasta, outFasta);
pDataArray->m->openOutputFile(pDataArray->outputMisMatches, outMisMatch);
pDataArray->m->openOutputFile(pDataArray->outputScrapFasta, outScrapFasta);
outMisMatch << "Name\tLength\tOverlap_Length\tOverlap_Start\tOverlap_End\tMisMatches\tNum_Ns\n";
- TrimOligos trimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, pDataArray->primers, pDataArray->barcodes);
+ Oligos oligos;
+ if (pDataArray->oligosfile != "") { oligos.read(pDataArray->oligosfile); }
+ int numFPrimers = oligos.getPairedPrimers().size();
+ int numBarcodes = oligos.getPairedBarcodes().size();
+
+
+ TrimOligos trimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, oligos.getPairedPrimers(), oligos.getPairedBarcodes());
+ TrimOligos* rtrimOligos = NULL;
+ if (pDataArray->reorient) {
+ rtrimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, oligos.getReorientedPairedPrimers(), oligos.getReorientedPairedBarcodes()); numBarcodes = oligos.getReorientedPairedBarcodes().size();
+ }
while ((!inFFasta.eof()) && (!inRFasta.eof())) {
rQual = new QualityScores(inRQual); pDataArray->m->gobble(inRQual);
}
+ Sequence findexBarcode("findex", "NONE"); Sequence rindexBarcode("rindex", "NONE");
+ if (thisfindexfile != "") {
+ Sequence temp(inFIndex); pDataArray->m->gobble(inFIndex);
+ findexBarcode.setAligned(temp.getAligned());
+ }
+
+ if (thisrindexfile != "") {
+ Sequence temp(inRIndex); pDataArray->m->gobble(inRIndex);
+ rindexBarcode.setAligned(temp.getAligned());
+ }
+
int barcodeIndex = 0;
int primerIndex = 0;
+ Sequence savedFSeq(fSeq.getName(), fSeq.getAligned()); Sequence savedRSeq(rSeq.getName(), rSeq.getAligned());
+ Sequence savedFindex(findexBarcode.getName(), findexBarcode.getAligned()); Sequence savedRIndex(rindexBarcode.getName(), rindexBarcode.getAligned());
+ QualityScores* savedFQual = NULL; QualityScores* savedRQual = NULL;
+ if (thisfqualfile != "") {
+ savedFQual = new QualityScores(fQual->getName(), fQual->getQualityScores());
+ savedRQual = new QualityScores(rQual->getName(), rQual->getQualityScores());
+ }
- if(pDataArray->barcodes.size() != 0){
+ if(numBarcodes != 0){
if (thisfqualfile != "") {
- success = trimOligos.stripBarcode(fSeq, rSeq, *fQual, *rQual, barcodeIndex);
+ if ((thisfindexfile != "") || (thisrindexfile != "")) {
+ success = trimOligos.stripBarcode(findexBarcode, rindexBarcode, *fQual, *rQual, barcodeIndex);
+ }else {
+ success = trimOligos.stripBarcode(fSeq, rSeq, *fQual, *rQual, barcodeIndex);
+ }
}else {
success = trimOligos.stripBarcode(fSeq, rSeq, barcodeIndex);
}
else{ currentSeqsDiffs += success; }
}
- if(pDataArray->primers.size() != 0){
+ if(numFPrimers != 0){
if (thisfqualfile != "") {
success = trimOligos.stripForward(fSeq, rSeq, *fQual, *rQual, primerIndex);
}else {
if (currentSeqsDiffs > pDataArray->tdiffs) { trashCode += 't'; }
+ if (pDataArray->reorient && (trashCode != "")) { //if you failed and want to check the reverse
+ int thisSuccess = 0;
+ string thisTrashCode = "";
+ int thisCurrentSeqsDiffs = 0;
+
+ int thisBarcodeIndex = 0;
+ int thisPrimerIndex = 0;
+
+ if(numBarcodes != 0){
+ if (thisfqualfile != "") {
+ if ((thisfindexfile != "") || (thisrindexfile != "")) {
+ thisSuccess = rtrimOligos->stripBarcode(savedFindex, savedRIndex, *savedFQual, *savedRQual, thisBarcodeIndex);
+ }else {
+ thisSuccess = rtrimOligos->stripBarcode(savedFSeq, savedRSeq, *savedFQual, *savedRQual, thisBarcodeIndex);
+ }
+ }else {
+ thisSuccess = rtrimOligos->stripBarcode(savedFSeq, savedRSeq, thisBarcodeIndex);
+ }
+ if(thisSuccess > pDataArray->bdiffs) { thisTrashCode += 'b'; }
+ else{ thisCurrentSeqsDiffs += thisSuccess; }
+ }
+
+ if(numFPrimers != 0){
+ if (thisfqualfile != "") {
+ thisSuccess = rtrimOligos->stripForward(savedFSeq, savedRSeq, *savedFQual, *savedRQual, thisPrimerIndex);
+ }else {
+ thisSuccess = rtrimOligos->stripForward(savedFSeq, savedRSeq, thisPrimerIndex);
+ }
+ if(thisSuccess > pDataArray->pdiffs) { thisTrashCode += 'f'; }
+ else{ thisCurrentSeqsDiffs += thisSuccess; }
+ }
+
+ if (thisCurrentSeqsDiffs > pDataArray->tdiffs) { thisTrashCode += 't'; }
+
+ if (thisTrashCode == "") {
+ trashCode = thisTrashCode;
+ success = thisSuccess;
+ currentSeqsDiffs = thisCurrentSeqsDiffs;
+ barcodeIndex = thisBarcodeIndex;
+ primerIndex = thisPrimerIndex;
+ savedFSeq.reverseComplement();
+ savedRSeq.reverseComplement();
+ fSeq.setAligned(savedFSeq.getAligned());
+ rSeq.setAligned(savedRSeq.getAligned());
+ if(thisfqualfile != ""){
+ savedFQual->flipQScores(); savedRQual->flipQScores();
+ fQual->setScores(savedFQual->getScores()); rQual->setScores(savedRQual->getScores());
+ }
+ }else { trashCode += "(" + thisTrashCode + ")"; }
+ }
+
//flip the reverse reads
rSeq.reverseComplement();
if (thisfqualfile != "") { rQual->flipQScores(); }
if (thisfqualfile != "") {
scores1 = fQual->getQualityScores();
scores2 = rQual->getQualityScores();
- delete fQual; delete rQual;
+ delete fQual; delete rQual; delete savedFQual; delete savedRQual;
}
int overlapStart = fSeq.getStartPos();
if(trashCode.length() == 0){
bool ignore = false;
if (pDataArray->createOligosGroup) {
- if(pDataArray->barcodes.size() != 0){
- string thisGroup = pDataArray->barcodeNameVector[barcodeIndex];
- if (pDataArray->primers.size() != 0) {
- if (pDataArray->primerNameVector[primerIndex] != "") {
- if(thisGroup != "") {
- thisGroup += "." + pDataArray->primerNameVector[primerIndex];
- }else {
- thisGroup = pDataArray->primerNameVector[primerIndex];
- }
- }
- }
-
- if (pDataArray->m->debug) { pDataArray->m->mothurOut(", group= " + thisGroup + "\n"); }
-
- int pos = thisGroup.find("ignore");
- if (pos == string::npos) {
- pDataArray->groupMap[fSeq.getName()] = thisGroup;
+ string thisGroup = oligos.getGroupName(barcodeIndex, primerIndex);
+ if (pDataArray->m->debug) { pDataArray->m->mothurOut(", group= " + thisGroup + "\n"); }
+
+ int pos = thisGroup.find("ignore");
+ if (pos == string::npos) {
+ pDataArray->groupMap[fSeq.getName()] = thisGroup;
- map<string, int>::iterator it = pDataArray->groupCounts.find(thisGroup);
- if (it == pDataArray->groupCounts.end()) { pDataArray->groupCounts[thisGroup] = 1; }
- else { pDataArray->groupCounts[it->first] ++; }
- }else { ignore = true; }
- }
+ map<string, int>::iterator it = pDataArray->groupCounts.find(thisGroup);
+ if (it == pDataArray->groupCounts.end()) { pDataArray->groupCounts[thisGroup] = 1; }
+ else { pDataArray->groupCounts[it->first] ++; }
+ }else { ignore = true; }
}else if (pDataArray->createFileGroup) {
int pos = pDataArray->group.find("ignore");
if (pos == string::npos) {
inRQual.close();
}
delete alignment;
+ if (pDataArray->reorient) { delete rtrimOligos; }
pDataArray->done = true;
if (pDataArray->m->control_pressed) { pDataArray->m->mothurRemove(pDataArray->outputFasta); pDataArray->m->mothurRemove(pDataArray->outputMisMatches); pDataArray->m->mothurRemove(pDataArray->outputScrapFasta); }
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