shenwei356/seqkit: 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"). Links OS Arch File, 中国镜像 Download Count Linux 32-bit seqkit_linux_386.tar.gz, 中国镜像 Linux 64-bit seqkit_linux_amd64.tar.gz, 中国镜像 Linux arm64 seqkit_linux_arm64.tar.gz, 中国镜像 macOS 64-bit seqkit_darwin_amd64.tar.gz, 中国镜像 macOS arm64 seqkit_darwin_arm64.tar.gz, 中国镜像 Windows 32-bit seqkit_windows_386.exe.tar.gz, 中国镜像 Windows 64-bit seqkit_windows_amd64.exe.tar.gz, 中国镜像 Please cite: W Shen, S Le, Y Li*, F Hu*. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLOS ONE. doi:10.1371/journal.pone.0163962. Notes please open an issuse to request binaries for other platforms. run seqkit version to check update !!! run seqkit genautocomplete to update shell autocompletion script !!