try {
string helpString = "";
helpString += "The chimera.check command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
- helpString += "This command was created using the algorythms described in CHIMERA_CHECK version 2.7 written by Niels Larsen. \n";
+ helpString += "This command was created using the algorithms described in CHIMERA_CHECK version 2.7 written by Niels Larsen. \n";
helpString += "The chimera.check command parameters are fasta, reference, processors, ksize, increment, svg and name.\n";
helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required unless you have a valid current fasta file. \n";
helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
#endif
//report progress
- if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
- count++;
+ if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n"); }
}
//report progress
- if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
+ if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n"); }
out.close();
inFASTA.close();
delete candidateSeq;
//report progress
- if((i+1) % 100 == 0){ cout << "Processing sequence: " << (i+1) << endl; m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n"); }
+ if((i+1) % 100 == 0){ cout << "Processing sequence: " << (i+1) << endl; }
}
//report progress
- if(num % 100 != 0){ cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n"); }
+ if(num % 100 != 0){ cout << "Processing sequence: " << num << endl; }
return 0;
}