WIP: DO NOT MERGE: Feature a/3295 option names
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.