void help() { m->mothurOut(getHelpString()); }
private:
- bool abort, allFiles, createGroup;
+ bool abort, allFiles, createGroup, trimOverlap;
string outputDir, ffastqfile, rfastqfile, align, oligosfile, rfastafile, ffastafile, rqualfile, fqualfile, file, format;
float match, misMatch, gapOpen, gapExtend;
int processors, longestBase, insert, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs, deltaq;
MothurOut* m;
float match, misMatch, gapOpen, gapExtend;
int count, insert, threadID, pdiffs, bdiffs, tdiffs, deltaq;
- bool allFiles, createGroup, done;
+ bool allFiles, createGroup, done, trimOverlap;
map<string, int> groupCounts;
map<string, string> groupMap;
vector<string> primerNameVector;
map<int, oligosPair> primers;
contigsData(){}
- contigsData(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 all, int tid) {
+ contigsData(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 all, bool to, int tid) {
files = f;
outputFasta = of;
outputMisMatches = om;
bdiffs = bdf;
tdiffs = tdf;
allFiles = all;
+ trimOverlap = to;
createGroup = cg;
threadID = tid;
deltaq = delt;
for (int i = overlapEnd; i < length; i++) { contig += seq1[i]; }
}
+ if (pDataArray->trimOverlap) { contig = contig.substr(overlapStart-1, oend-oStart); if (contig.length() == 0) { trashCode += "l"; } }
+
if(trashCode.length() == 0){
bool ignore = false;
if (pDataArray->createGroup) {