string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
- string getOutputPattern(string);
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Chops.seqs"; }
string getDescription() { return "trim sequence length"; }
linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
};
- string fastafile, outputDir, keep;
+ string fastafile, outputDir, keep, namefile, groupfile, countfile;
bool abort, countGaps, Short;
int numbases, processors;
vector<string> outputNames;
string outFasta, outAccnos, keep;
unsigned long long start;
unsigned long long end;
- int numbases;
+ int numbases, count;
bool countGaps, Short, wroteAccnos;
MothurOut* m;
string namefile;
bool done = false;
bool wroteAccnos = false;
- int count = 0;
+ pDataArray->count = 0;
for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
outAcc << seq.getName() << endl;
pDataArray->wroteAccnos = true;
}
- count++;
+ pDataArray->count++;
}
//report progress
- if((count) % 1000 == 0){ pDataArray->m->mothurOut(toString(count)); pDataArray->m->mothurOutEndLine(); }
+ if((pDataArray->count) % 1000 == 0){ pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine(); }
}
//report progress
- if((count) % 1000 != 0){ pDataArray->m->mothurOut(toString(count)); pDataArray->m->mothurOutEndLine(); }
+ if((pDataArray->count) % 1000 != 0){ pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine(); }
in.close();