lexicmap utils subseq

$ lexicmap utils subseq -h
Extract subsequence via 1) reference name, sequence ID, position and strand, or 2) search result

Input:
  - Manually specify reference name, sequence ID, region, and strand.
  - Or give the search result file generated by "lexicmap search".
    - If the search result data has no header row, after filtering using tools like awk,
      please switch on the flag -H/--no-header-row.
    - Results with --show-sseq-idx are supported. Exact sequence IDs take precedence;
      chunk/sequence prefixes are removed only when no exact ID is found.
    - Results with --show-genome-name or --show-species-name are supported. Exact genome
      IDs take precedence; otherwise, the name prefix is removed only if one indexed
      genome ID matches. Ambiguous prefixes are errors (skipped with --ignore-err).

Tips:
  - The aligned region can be extended with -U/--upstream and/or -D/--downstream.
  - After extension, a start beyond the sequence length is an error; an oversized end is clipped.
    In search-result mode, -e/--ignore-err skips records that cannot be extracted.
  - If the search results are merged from multiple indexes, it would report error
    "reference name not found". You can switch on -e/--ignore-err to ignore this.

Output:
  - FASTA format, with a sequence ID in the format of "seqid:begin-end:strand".
    The begin and end are positions in the indexed sequence, and begin is <= end.
    End coordinates reflect clipping at the sequence boundary.
    And the sequence is reverse-complementary when the strand is "-".

Attention:
  1. When manually specifying the genome and region, the option -s/--seq-id is optional.
     1) If given, the positions are these in the original sequence.
     2) If not given, the positions are these in the concatenated sequence.
  2. All degenerate bases in reference genomes were converted to the lexicographic first bases.
     E.g., N was converted to A. Therefore, consecutive A's in output might be N's in the genomes.

Usage:
  lexicmap utils subseq [flags]

Flags:
  -b, --buffer-size string     ► Size of buffer, supported unit: K, M, G. You need increase the value
                               when "bufio.Scanner: token too long" error reported (default "20M")
  -D, --downstream int         ► Extract extra N bp on the downstream of the aligned/specified region.
  -h, --help                   help for subseq
  -e, --ignore-err             ► Ignore errors such as 'reference name not found' or 'failed to
                               extract subsequence'. Switch on this flag if search results are merged
                               from multiple indexes.
  -d, --index string           ► Index directory created by "lexicmap index".
  -w, --line-width int         ► Line width of sequence (0 for no wrap). (default 60)
      --max-open-files int     ► File budget for subsequence extraction, including 9 reserved
                               descriptors (minimum: 10). Limits reader concurrency; readers open on
                               demand if batch pools do not fit. Set "ulimit -n" at least this high.
                               (default 1024)
  -H, --no-header-row          ► The search result file has no header row, this happens when using
                               tools like awk to filter the file.
  -o, --out-file string        ► Out file, supports the ".gz" suffix ("-" for stdout). (default "-")
  -n, --ref-name string        ► Reference name.
  -r, --region string          ► Region of the subsequence (1-based).
  -R, --revcom                 ► Extract subsequence on the negative strand.
  -f, --search-result string   ► Use search result file from "lexicmap search" as input. It can be "-"
                               to accept filtered result from stdin
  -s, --seq-id string          ► Sequence ID. If the value is empty, the positions in the region are
                               treated as that in the concatenated sequence.
  -U, --upstream int           ► Extract extra N bp on the upstream of the aligned/specified region.

Global Flags:
      --force-gzip-output    ► Gzip-compress result output regardless of the filename, including stdout.
  -X, --infile-list string   ► File of input file list (one file per line). If given, they are
                             appended to files from CLI arguments.
      --log string           ► Log file.
      --quiet                ► Do not print any verbose information. But you can write them to a file
                             with --log.
  -j, --threads int          ► Number of CPU cores to use. By default, it uses all available cores.
                             (default 16)

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