Commit 3c243c26 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

vidjil.cpp: reads_file argument, required, help message

parent 77d8a704
......@@ -307,8 +307,13 @@ int main (int argc, char **argv)
// cerr << "Usage: " << progname << " [options] <reads.fa/.fq/.gz>" << endl << endl;
group = "Files";
app.add_option("reads", f_reads, "reads.fa/.fq/.gz") -> group(group) -> set_type_name("FILE");
app.add_option("reads_file", f_reads, R"Z(reads file, in one of the following formats:
- FASTA (.fa/.fasta, .fa.gz/.fasta.gz)
- FASTQ (.fq/.fastq, .fq.gz/.fastq.gz)
- BAM (.bam)
Paired-end reads should be merged before given as an input to vidjil-algo.
-> required() -> set_type_name("");
group = "Command selection";
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