vector<string> setParameters();
string getCommandName() { return "trim.flows"; }
string getCommandCategory() { return "Sequence Processing"; }
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Trim.flows"; }
string getDescription() { return "trim.flows"; }
vector<unsigned long long> getFlowFileBreaks();
int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >);
int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
-
+ string reverseOligo(string);
+
vector<string> outputNames;
set<string> filesToRemove;
bool allFiles;
int processors;
int numFPrimers, numRPrimers;
- int numLinkers, numSpacers;
-
- int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
+ int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
int numFlows;
float signal, noise;
bool fasta;
map<string, int> barcodes;
map<string, int> primers;
vector<string> revPrimer;
+ vector<string> linker;
+ vector<string> spacer;
vector<string> primerNameVector; //needed here?
vector<string> barcodeNameVector; //needed here?
};
/**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
#else
static DWORD WINAPI MyTrimFlowThreadFunction(LPVOID lpParam){
trimFlowData* pDataArray;
flowData.printFlows(trimFlowFile);
- if(pDataArray->fasta) { currSeq.printSequence(fastaFile); }
+ if(pDataArray->fasta) { currSeq.setAligned(currSeq.getUnaligned()); currSeq.printSequence(fastaFile); }
if(pDataArray->allFiles){
ofstream output;