SeqKit v2.4.0

Changes

• SeqKit v2.4.0 - 2023-03-17
  • seqkit:
    • support bzip2 format. #361
    • support setting compression level for gzip, zstd, and bzip2 format via --compress-level. #320
    • the global flag --infile-list accepts stdin (-) now.
    • wrap the help message of flags.
  • seqkit locate:
    • do not remove embeded regions when searching with regular expressions. #368
  • seqkit amplicon:
    • fix BED coordinates for amplicons found in the minus strand. #367
  • seqkit split:
    • fix forgetting to add extension for --two-pass. #332
  • seqkit stats:
    • fix compute Q1 and Q3 of sequence length for one record. #353
  • seqkit grep:
    • fix count number (-C) for matching with mismatch (-m > 0). #370
  • seqkit replace:
    • add some flags to match partly records to edit; these flags are transplanted from seqkit grep. #348
  • seqkit faidx:
    • allow empty lines at the end of sequences.
  • seqkit faidx/sort/shuffle/split/subseq:
    • new flag -U/--update-faidx: update the FASTA index file if it exists, to guarantee the index file matches the FASTA files. #364
    • improve log info and update help message. #365
  • seqkit seq:
    • allow filtering sequences of length zero. thanks to @penglbio.
  • seqkit rename:
    • new flag -s/--separator for setting separator between original ID/name and the counter (default "_"). #360
    • new flag -N/--start-num for setting starting count number for duplicated IDs/names (default 2). #360
    • new flag -1/--rename-1st-rec for renaming the first record as well. #360
    • do not append space if there's no description after the sequene ID.
  • seqkit sliding:
    • new flag -S/--suffix for change the suffix added to the sequence ID (default: "_sliding").