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See #3295 (closed).

Usage: ./vidjil-algo [OPTIONS] reads_file

  reads_file                  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.
                 

Command selection
  -c COMMAND                  command
  		clones  	 locus detection, window extraction, clone clustering (default command, most efficient, all outputs)
  		windows  	 locus detection, window extraction
  		segment  	 detailed V(D)J designation (not recommended)
  		germlines  	 statistics on k-mers in different germlines

Input
  -x, --first-reads INT       maximal number of reads to process ('all': no limit, default), only first reads
  -X, --sampled-reads INT     maximal number of reads to process ('all': no limit, default), sampled reads

Germline presets (at least one -g or -V/(-D)/-J option must be given)
  -g, --germline GERMLINES ...
                              
         -g <.g FILE>(:FILTER)
                    multiple locus/germlines, with tuned parameters.
                    Common values are '-g germline/homo-sapiens.g' or '-g germline/mus-musculus.g'
                    The list of locus/recombinations can be restricted, such as in '-g germline/homo-sapiens.g:IGH,IGK,IGL'
         -g PATH
                    multiple locus/germlines, shortcut for '-g PATH/homo-sapiens.g',
                    processes human TRA, TRB, TRG, TRD, IGH, IGK and IGL locus, possibly with incomplete/unusal recombinations
  -V FILE ...                 custom V germline multi-fasta file(s)
  -D FILE ...                 custom D germline multi-fasta file(s), analyze into V(D)J components
  -J FILE ...                 custom V germline multi-fasta file(s)
  -2                          try to detect unexpected recombinations

Limits to report and to analyze clones (second pass)
  -r, --min-reads INT=5       minimal number of reads supporting a clone
  --min-ratio FLOAT=0         minimal percentage of reads supporting a clone
  --max-clones INT            maximal number of output clones ('all': no maximum, default)
  -y, --max-consensus INT=100 maximal number of clones computed with a consensus sequence ('all': no limit)
  -z, --max-designations INT=100
                              maximal number of clones to be analyzed with a full V(D)J designation ('all': no limit, do not use)
  --all                       reports and analyzes all clones
                              (--min-reads 1 --min-ratio 0 --max-clones all --max-clones-with-consensus all --max-clones-with-analysis all),
                              to be used only on very small datasets (for example --all -X 20)

Clone analysis (second pass)
  -d, --several-D             try to detect several D (experimental)
  -3, --cdr3                  CDR3/JUNCTION detection (requires gapped V/J germlines)

Detailed output per read (generally not recommended, large files, but may be used for filtering, as in -uu -X 1000)
  -U, --out-analyzed          output analyzed reads (in .segmented.vdj.fa file)
  -u, --out-unanalyzed        
        -u          output unanalyzed reads, gathered by cause, except for very short and 'too few V/J' reads (in *.fa files)
        -uu         output unanalyzed reads, gathered by cause, all reads (in *.fa files) (use only for debug)
        -uuu        output unanalyzed reads, all reads, including a .unsegmented.vdj.fa file (use only for debug)
  --out-reads                 output all reads by clones (clone.fa-*), to be used only on small datasets

Output
  -o, --out-dir PATH=./out/   output directory
  -b, --out-base STRING       output basename (by default basename of the input file)
  -v, --verbose               verbose mode

Help
  -h, --help                  help
  -H, --help-advanced         help, including advanced and experimental options
                              The full help is available in the doc/algo.org file.