process++;
}else if (pid == 0){
string locationsFile = toString(getpid()) + ".temp";
- num = driverPcr(filename, goodFileName + toString(getpid()) + ".temp", badFileName + toString(getpid()) + ".temp", locationsFile, badSeqNames, lines[process], pstart, pend, adjustNeeded);
+ num = driverPcr(filename, goodFileName + toString(getpid()) + ".temp", badFileName + toString(getpid()) + ".temp", locationsFile, badSeqNames, lines[process], pstart, adjustNeeded);
//pass numSeqs to parent
ofstream out;
string tempFile = filename + toString(getpid()) + ".num.temp";
m->openOutputFile(tempFile, out);
- out << pstart << '\t' << pend << '\t' << adjustNeeded << endl;
+ out << pstart << '\t' << adjustNeeded << endl;
out << num << '\t' << badSeqNames.size() << endl;
for (set<string>::iterator it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
out << (*it) << endl;
}
string locationsFile = toString(getpid()) + ".temp";
- num = driverPcr(filename, goodFileName, badFileName, locationsFile, badSeqNames, lines[0], pstart, pend, adjustNeeded);
+ num = driverPcr(filename, goodFileName, badFileName, locationsFile, badSeqNames, lines[0], pstart, adjustNeeded);
//force parent to wait until all the processes are done
for (int i=0;i<processIDS.size();i++) {
string tempFile = filename + toString(processIDS[i]) + ".num.temp";
m->openInputFile(tempFile, in);
int numBadNames = 0; string name = "";
- int tpstart = -1; int tpend = -1; bool tempAdjust = false;
+ int tpstart = -1; bool tempAdjust = false;
if (!in.eof()) {
- in >> tpstart >> tpend >> tempAdjust; m->gobble(in);
+ in >> tpstart >> tempAdjust; m->gobble(in);
if (tempAdjust) { adjustNeeded = true; }
if (tpstart != -1) {
if (tpstart != pstart) { adjustNeeded = true; }
if (tpstart < pstart) { pstart = tpstart; } //smallest start
}
- if (tpend != -1) {
- if (tpend != pend) { adjustNeeded = true; }
- if (tpend > pend) { pend = tpend; } //largest end
- }
int tempNum = 0; in >> tempNum >> numBadNames; num += tempNum; m->gobble(in);
}
for (int j = 0; j < numBadNames; j++) {
}
//do your part
- num = driverPcr(filename, (goodFileName+toString(processors-1)+".temp"), (badFileName+toString(processors-1)+".temp"), (locationsFile+toString(processors-1)+".temp"), badSeqNames, lines[processors-1], pstart, pend, adjustNeeded);
+ num = driverPcr(filename, (goodFileName+toString(processors-1)+".temp"), (badFileName+toString(processors-1)+".temp"), (locationsFile+toString(processors-1)+".temp"), badSeqNames, lines[processors-1], pstart, adjustNeeded);
processIDS.push_back(processors-1);
//Wait until all threads have terminated.
if (pDataArray[i]->pstart != pstart) { adjustNeeded = true; }
if (pDataArray[i]->pstart < pstart) { pstart = pDataArray[i]->pstart; }
} //smallest start
- if (pDataArray[i]->pend != -1) {
- if (pDataArray[i]->pend != pend) { adjustNeeded = true; }
- if (pDataArray[i]->pend > pend) { pend = pDataArray[i]->pend; }
- } //largest end
-
+
for (set<string>::iterator it = pDataArray[i]->badSeqNames.begin(); it != pDataArray[i]->badSeqNames.end(); it++) { badSeqNames.insert(*it); }
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
}
#endif
- if (fileAligned && adjustNeeded) { adjustDots(goodFileName, locationsFile, pstart, pend); }
+
+
+
+ if (fileAligned) {
+ //find pend - pend is the biggest ending value, but we must account for when we adjust the start. That adjustment may make the "new" end larger then the largest end. So lets find out what that "new" end will be.
+ ifstream inLocations;
+ m->openInputFile(locationsFile, inLocations);
+
+ while(!inLocations.eof()) {
+
+ if (m->control_pressed) { break; }
+
+ string name = "";
+ int thisStart = -1; int thisEnd = -1;
+ if (primers.size() != 0) { inLocations >> name >> thisStart; m->gobble(inLocations); }
+ if (revPrimer.size() != 0) { inLocations >> name >> thisEnd; m->gobble(inLocations); }
+ else { pend = -1; break; }
+
+ int myDiff = 0;
+ if (pstart != -1) {
+ if (thisStart != -1) {
+ if (thisStart != pstart) { myDiff += (thisStart - pstart); }
+ }
+ }
+
+ int myEnd = thisEnd + myDiff;
+ //cout << name << '\t' << thisStart << '\t' << thisEnd << " diff = " << myDiff << '\t' << myEnd << endl;
+
+ if (thisEnd != -1) {
+ if (myEnd > pend) { pend = myEnd; }
+ }
+
+ }
+ inLocations.close();
+
+ adjustDots(goodFileName, locationsFile, pstart, pend);
+ }
return num;
}
//**********************************************************************************************************************
-int PcrSeqsCommand::driverPcr(string filename, string goodFasta, string badFasta, string locationsName, set<string>& badSeqNames, linePair filePos, int& pstart, int& pend, bool& adjustNeeded){
+int PcrSeqsCommand::driverPcr(string filename, string goodFasta, string badFasta, string locationsName, set<string>& badSeqNames, linePair filePos, int& pstart, bool& adjustNeeded){
try {
ofstream goodFile;
m->openOutputFile(goodFasta, goodFile);
bool done = false;
int count = 0;
set<int> lengths;
- vector< set<int> > locations; //locations[0] = beginning locations, locations[1] = ending locations
- locations.resize(2);
+ set<int> locations; //locations[0] = beginning locations,
//pdiffs, bdiffs, primers, barcodes, revPrimers
map<string, int> faked;
if(goodSeq == 1) {
currSeq.printSequence(goodFile);
if (m->debug) { m->mothurOut("[DEBUG]: " + locationsString + "\n"); }
+ if (thisPStart != -1) { locations.insert(thisPStart); }
if (locationsString != "") { locationsFile << locationsString; }
- if (thisPStart != -1) { locations[0].insert(thisPStart); }
- if (thisPEnd != -1) { locations[1].insert(thisPEnd); }
}
else {
badSeqNames.insert(currSeq.getName());
if (m->debug) { m->mothurOut("[DEBUG]: fileAligned = " + toString(fileAligned) +'\n'); }
if (fileAligned && !keepdots) { //print out smallest start value and largest end value
- if ((locations[0].size() > 1) || (locations[1].size() > 1)) { adjustNeeded = true; }
- if (primers.size() != 0) { set<int>::iterator it = locations[0].begin(); pstart = *it; }
- if (revPrimer.size() != 0) { set<int>::reverse_iterator it2 = locations[1].rbegin(); pend = *it2; }
+ if (locations.size() > 1) { adjustNeeded = true; }
+ if (primers.size() != 0) { set<int>::iterator it = locations.begin(); pstart = *it; }
}
return count;
set<int> lengths;
//cout << pstart << '\t' << pend << endl;
+ //if (pstart > pend) { //swap them
while(!inFasta.eof()) {
if(m->control_pressed) { break; }
int thisStart = -1; int thisEnd = -1;
if (primers.size() != 0) { inLocations >> name >> thisStart; m->gobble(inLocations); }
if (revPrimer.size() != 0) { inLocations >> name >> thisEnd; m->gobble(inLocations); }
+
+
//cout << seq.getName() << '\t' << thisStart << '\t' << thisEnd << '\t' << seq.getAligned().length() << endl;
//cout << seq.getName() << '\t' << pstart << '\t' << pend << endl;
//cout << "final lengths = \n";
//for (set<int>::iterator it = lengths.begin(); it != lengths.end(); it++) {
- // cout << *it << endl;
+ //cout << *it << endl;
+ // cout << lengths.count(*it) << endl;
// }
return 0;
else if (c == 32 || c == 9){;} //space or tab
}
primers[oligo] = primerCount; primerCount++;
+ //cout << "for oligo = " << oligo << endl;
}else if(type == "REVERSE"){
string oligoRC = reverseOligo(oligo);
revPrimer.push_back(oligoRC);
- //cout << "oligo = " << oligo << " reverse = " << oligoRC << endl;
+ //cout << "rev oligo = " << oligo << " reverse = " << oligoRC << endl;
}else if(type == "BARCODE"){
- inOligos >> group;
+ inOligos >> group;
+ }else if(type == "PRIMER"){
+ m->gobble(inOligos);
+ primers[oligo] = primerCount; primerCount++;
+
+ string roligo="";
+ inOligos >> roligo;
+
+ for(int i=0;i<roligo.length();i++){
+ roligo[i] = toupper(roligo[i]);
+ if(roligo[i] == 'U') { roligo[i] = 'T'; }
+ }
+ revPrimer.push_back(reverseOligo(roligo));
+
+ // get rest of line in case there is a primer name
+ while (!inOligos.eof()) {
+ char c = inOligos.get();
+ if (c == 10 || c == 13 || c == -1){ break; }
+ else if (c == 32 || c == 9){;} //space or tab
+ }
+ //cout << "prim oligo = " << oligo << " reverse = " << roligo << endl;
}else if((type == "LINKER")||(type == "SPACER")) {;}
- else{ m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, linker, spacer and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else{ m->mothurOut(type + " is not recognized as a valid type. Choices are primer, forward, reverse, linker, spacer and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); m->control_pressed = true; }
}
m->gobble(inOligos);
}
//check for groups that have been eliminated
CountTable ct;
if (ct.testGroups(goodCountFile)) {
- ct.readTable(goodCountFile, true);
+ ct.readTable(goodCountFile, true, false);
ct.printTable(goodCountFile);
}
projects / mothur.git / blobdiff