Command Line Interface

You can alos run Haplotype-Lso locally from the command line.

Note

This section needs some extension.

$ hlso cli \
    [--sample-name-from-file] \
    [--sample-regex REGEX] \
    [--output OUTPUT] \
    seq_file [seq_file ...]

This will read all sequence files seq_file (can be FASTA, FASTQ, AB1, SCF), perform conversion to FASTA (if needed) and then perform a haplotyping. When provided, the result will be written to the XLSX file OUTPUT.

You can override the regular expression to extract the sample name and region from the query name with --sample-regex.

By default, the query sequence names are taken from their identifier. As this is hard for the binary files AB1 and SCF, you can also configure Haplotype-Lso to use the file names (without extension) as the sample names. This is the behaviour from the web frontend.