SeqKit v0.5.2

Changelog

• seqkit stats -a and seqkit seq -g -G: change default gap letters from '- ' to '- .'

• seqkit subseq: fix bug of range overflow when using -d/--down-stream
  or -u/--up-stream for retieving subseq using BED (--beb) or GTF (--gtf) file.

• seqkit locate: add flag -G/--non-greedy, non-greedy mode,
  faster but may miss motifs overlaping with others. Example:

  • greedy mode (default)

       $ echo -e '>seq\nACGACGACGA' | seqkit locate -p ACGA | csvtk -t pretty
       seqID   patternName   pattern   strand   start   end   matched
       seq     ACGA          ACGA      +        1       4     ACGA
       seq     ACGA          ACGA      +        4       7     ACGA
       seq     ACGA          ACGA      +        7       10    ACGA
    

  • non-greedy mode (-G)

      $ echo -e '>seq\nACGACGACGA' | seqkit locate -p ACGA -G | csvtk -t pretty
      seqID   patternName   pattern   strand   start   end   matched
      seq     ACGA          ACGA      +        1       4     ACGA
      seq     ACGA          ACGA      +        7       10    ACGA