diff --git a/src/FQReport.cpp b/src/FQReport.cpp index c113a78d2a30c62fe436a921c957873d7cd27cb1..70247d3c6b68f9613029663d3348a9174fbd8456 100755 --- a/src/FQReport.cpp +++ b/src/FQReport.cpp @@ -41,22 +41,24 @@ using namespace std; void usage(int status) { - cout<<" FQreport 1.0 Copyright (C) 2021 Institut Pasteur"<<endl; cout<<endl; - cout<<" USAGE: fqreport [-i <infile>] [-o <outfile>] [-f <name>] [-p <offset>] [-h]"<<endl; + cout<<"FQreport 1.0 Copyright (C) 2021 Institut Pasteur"<<endl; cout<<endl; - cout<<" OPTIONS:"<<endl; - cout<<" -i <file> input file in FASTQ format (default: standard input)"<<endl; - cout<<" -f <string> sample name (default: file name set using option -i)"<<endl; - cout<<" -o <file> output file name (default: standard output)"<<endl; - cout<<" -p <33|64> Phred offset (default: 33)"<<endl; - cout<<" -h print this help and exit"<<endl; + cout<<"USAGE: fqreport [-i <infile>] [-o <outfile>] [-f <name>] [-p <offset>] [-h]"<<endl; + cout<<endl; + cout<<"OPTIONS:"<<endl; + cout<<" -i <file> input file in FASTQ format (default: standard input)"<<endl; + cout<<" -f <string> sample name (default: file name set using option -i)"<<endl; + cout<<" -o <file> output file name (default: standard output)"<<endl; + cout<<" -p <33|64> Phred offset (default: 33)"<<endl; + cout<<" -h print this help and exit"<<endl; + cout<<endl; + cout<<"EXAMPLES:"<<endl; + cout<<" fqreport -i infile.fastq -o report.txt"<<endl; + cout<<" fqreport -i infile.fastq -f sample -p 64"<<endl; + cout<<" cat infile.fastq | fqreport -f sample -o report.txt"<<endl; + cout<<" gunzip -c infile.fastq.gz | fqreport"<<endl; cout<<endl; - cout<<" EXAMPLES:"<<endl; - cout<<" fqreport -i infile.fastq -o report.txt"<<endl; - cout<<" fqreport -i infile.fastq -f sample -p 64"<<endl; - cout<<" cat infile.fastq | fqreport -f sample -o report.txt"<<endl; - cout<<" gunzip -c infile.fastq.gz | fqreport"<<endl; exit(status); }