Usage: xloci [OPTIONS] --regions <REGIONS> --outdir <OUTDIR>

Options:
 -s, --sequence <SEQUENCE>
         Path to genome sequence file (.fa, .fa.gz, or .2bit); reads from stdin when omitted
 -r, --regions <REGIONS>
         Path to genomic regions file (BED, GTF, or GFF format)
 -o, --outdir <OUTDIR>
         Output directory for extracted sequences
 -c, --chunks <CHUNKS>
         Number of records per parallel processing chunk [default: 1000]
 -u, --upstream-flank <UPSTREAM_FLANK>
         Bases to extend upstream of features [default: 0]
 -d, --downstream-flank <DOWNSTREAM_FLANK>
         Bases to extend downstream of features [default: 0]
 -f, --feature <FEATURE>
         Type of genomic feature to extract [default: exon] [possible values: transcript, exon, intron, cds, utr]
 -I, --ignore-errors
         Continue processing on errors instead of panicking
 -L, --level <LEVEL>
         Logging verbosity level [default: info]
 -p, --prefix <PREFIX>
         Stem for output FASTA files (writes <prefix>.fa or <prefix>.fa.gz) [default: output]
 -X, --translate
         Translate sequences to protein
 -U, --unmask
         Convert soft-masked bases to uppercase in output
 -S, --split-extraction
         Emit one output record per extracted feature piece
     --as-tsv
         Write tab-separated output instead of FASTA
     --add-tab
         Separate flank columns in TSV output (requires --as-tsv and at least one flank)
 -G, --generic-id
         Use genomic coordinates as identifiers instead of record names
 -A, --as-chunk
         Keep chunk outputs and skip merging into a single file
 -B, --include-bed
         Also emit chunked BED outputs (requires --as-chunk)
 -Z, --compress
         Gzip-compress output files
 -t, --threads <THREADS>
         Number of threads [default: 16]
 -h, --help
         Print help
 -V, --version
         Print version