diff --git a/src/ROCKparams.cpp b/src/ROCKparams.cpp index af0f71386163ec9b5c4bb5547c2cfb765fd6e489..bb01e22cbfb4ef4621bc775c474fce10e285c747 100755 --- a/src/ROCKparams.cpp +++ b/src/ROCKparams.cpp @@ -41,27 +41,27 @@ cout<<"USAGE: rock [options] [files]"<<endl; cout<<endl; cout<<"OPTIONS:"<<endl; cout<<" -i <file> file containing the name(s) of the input FASTQ file(s) to"<<endl; -cout<<" process; single-end: one file name per line; paired-end:"<<endl; -cout<<" two file names per line separated by a comma; up to 15"<<endl; -cout<<" FASTQ file names can be specified; of note, input file"<<endl; -cout<<" name(s) can also be specified as program argument(s)"<<endl; +cout<<" process; single-end: one file name per line; paired-end:"<<endl; +cout<<" two file names per line separated by a comma; up to 15"<<endl; +cout<<" FASTQ file names can be specified; of note, input file"<<endl; +cout<<" name(s) can also be specified as program argument(s)"<<endl; cout<<" -o <file> file containing the name(s) of the output FASTQ file(s);"<<endl; -cout<<" FASTQ file name(s) should be structured in the same way as"<<endl; -cout<<" the file specified in option -i."<<endl; +cout<<" FASTQ file name(s) should be structured in the same way as"<<endl; +cout<<" the file specified in option -i."<<endl; cout<<" -k <int> k-mer length (default 25)"<<endl; cout<<" -c <int> lower-bound k-mer coverage depth threshold (default: 0)"<<endl; cout<<" -C <int> upper-bound k-mer coverage depth threshold (default: 70)"<<endl; cout<<" -l <int> number of hashing function(s) (default: 4)"<<endl; cout<<" -n <int> expected total number of distinct k-mers within the input"<<endl; -cout<<" read sequences; not compatible with option -l."<<endl; +cout<<" read sequences; not compatible with option -l."<<endl; cout<<" -f <float> maximum expected false positive probability when computing"<<endl; -cout<<" the optimal number of hashing functions from the number of"<<endl; -cout<<" distinct k-mers specified with option -n (default: 0.05)."<<endl; +cout<<" the optimal number of hashing functions from the number of"<<endl; +cout<<" distinct k-mers specified with option -n (default: 0.05)."<<endl; cout<<" -q <int> sets as valid only k-mers made up of nucleotides with"<<endl; -cout<<" Phred score (+33 offset) above this cutoff (default: 0)"<<endl; +cout<<" Phred score (+33 offset) above this cutoff (default: 0)"<<endl; cout<<" -m <int> minimum number of valid k-mer(s) to consider a read; all"<<endl; -cout<<" non-considered reads are written into output file(s) with"<<endl; -cout<<" extension undefined.fastq (default: 1)"<<endl; +cout<<" non-considered reads are written into output file(s) with"<<endl; +cout<<" extension undefined.fastq (default: 1)"<<endl; cout<<" -v verbose mode"<<endl; cout<<" -h prints this message and exit"<<endl; exit(status);