Build with
cargo build -r
Run with
./target/release/distle --help
Usage: distle [OPTIONS] <INPUT> <OUTPUT>
Arguments:
<INPUT>
The input file or '-' for stdin
<OUTPUT>
The output file or '-' for stdout
Options:
-i, --input-format <INPUT_FORMAT>
The format of the input file
[default: fasta]
Possible values:
- cgmlst: A cgmlst table with allele numbers. Optimized for ChewBBACA output
- cgmlst-hash: A cgmlst table with SHA1 hashes of the nucleotide of the alleles
- fasta: An alignment of nucleotide sequences in FASTA format
- fasta-all: An alignment of nucleotide sequences in FASTA format. Counts all differences and not just [ACTG]
-o, --output-format <OUTPUT_FORMAT>
The format of the output file
[default: tabular]
Possible values:
- tabular: Output the distances in a tabular long format
- phylip: Output the distances in a Phylip format
--precomputed-distances <PRECOMPUTED_DISTANCES>
A file with precomputed distances that don't have to be calculated again. The file should be in tabular long format and have the separator as specified by the output-sep flag
--input-sep <INPUT_SEP>
The separator character for the input file. Relevant for tabular input files
[default: "\t"]
--output-sep <OUTPUT_SEP>
The separator character for the output file
[default: "\t"]
-m, --output-mode <OUTPUT_MODE>
The output mode
[default: lower-triangle]
Possible values:
- lower-triangle: Only output the lower triangle of the distance matrix since it is diagonally symmetric
- full: Output the full distance matrix
-d, --maxdist <MAXDIST>
If set, distance calculations will be stopped when this distance is reached. Useful for large datasets
-t, --threads <THREADS>
Number of threads to use. If not set, all available threads will be used
-s, --skip-header
Skip the header line of the input file. Relevant for tabular input files
-v, --verbose
Enable verbose mode. Outputs debug messages and calculation times
-h, --help
Print help (see a summary with '-h')
-V, --version
Print version