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@shenwei356 shenwei356 released this Jul 13, 2020 · 2 commits to master since this release

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  • run seqkit genautocomplete to update Bash completion !!!
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Linux 32-bit seqkit_linux_386.tar.gz,
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Linux 64-bit seqkit_linux_amd64.tar.gz,
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OS X 32-bit seqkit_darwin_386.tar.gz,
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OS X 64-bit seqkit_darwin_amd64.tar.gz,
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Windows 32-bit seqkit_windows_386.exe.tar.gz,
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Windows 64-bit seqkit_windows_amd64.exe.tar.gz,
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Assets 8

@shenwei356 shenwei356 released this Jul 9, 2020 · 5 commits to master since this release

Changes

Assets 8

@shenwei356 shenwei356 released this Jul 7, 2020 · 8 commits to master since this release

Changes

  • SeqKit v0.13.0 Github Releases (by Release)
    • seqkit: fix a rare FASTA/Q parser bug. #127
    • seqkit seq: output sequence or quality in single line when -s/--seq or -q/--qual is on. #132
    • seqkit translate: delete debug info, #133, and fix typo. #134
    • seqkit split2: tiny performance improvement. #137
    • seqkit stats: new flag -i/--stdin-label for replacing default "-" for stdin. #139
    • seqkit fx2tab: new flag -s/--seq-hash for printing hash of sequence (case sensitive). #144
    • seqkit amplicon:
      • fix bug of missing searching reverse strand. #140
      • supporting degenerate bases now. #83
      • new flag -p/--primer-file for reading list of primer pairs. #142
      • new flag --bed for outputing in BED6+1 format. #141
    • New features and improvements by @bsipos. #130, #147
      • new command seqkit scat, for real-time robust concatenation of fastx files.
      • Rewrote the parser behind the sana subcommand, now it supports robust parsing of fasta file as well.
      • Added a "toolbox" feature to the bam subcommand (-T), which is a collection of filters acting on streams of BAM records configured through a YAML string (see the docs for more).
      • Added the SEQKIT_THREADS environmental variable to override the default number of threads.
Assets 8

@shenwei356 shenwei356 released this Apr 21, 2020 · 27 commits to master since this release

Changes

  • SeqKit v0.12.1 Github Releases (by Release)
    • seqkit bam: add colorised and pretty printed output, by @bsipos. #110
    • seqkit locate/grep: fix bug of -m, when query contains letters not in subject sequences. #124
    • seqkit split2: new flag -l/--by-length for splitting into chunks of N bases.
    • seqkit fx2tab:
      • new flag -I/--case-sensitive for calculating case sensitive base content. #108
      • add missing column name for averge quality for -H -q. #115
      • fix output of -n/--only-name, do not write empty columns of sequence and quality. #104, #115
    • seqkit seq: new flag -k/--color: colorize sequences.
Assets 8

@shenwei356 shenwei356 released this Feb 18, 2020 · 130 commits to master since this release

Changes

  • SeqKit v0.12.0 Github Releases (by Release)
    • seqkit:
      • fix checking input file existence.
      • new global flag --infile-list for long list of input files, if given, they are appended to files from cli arguments.
    • seqkit faidx: supporting "truncated" (no ending newline charactor) file.
    • seqkit seq:
      • do not force switching on -g when using -m/-M.
      • show recommendation if flag -t/--seq-type is not DNA/RNA when computing complement sequence. #103
    • seqkit translate: supporting multiple frames. #96
    • seqkit grep/locate:
      • add detection and warning for space existing in search pattern/sequence.
      • speed improvement (2X) for -m/--max-mismatch. shenwei356/bwt/issues/3
    • seqkit locate:
      • new flag -M/--hide-matched for hiding matched sequences. #98
      • new flag -r/--use-regexp for explicitly using regular expression, so improve speed of default index operation. And you have to switch this on if using regexp now.
        #101
      • new flag -F/--use-fmi for improving search speed for lots of sequence patterns.
    • seqkit rename: making IDs unique across multiple files, and can write into multiple files. #100
    • seqkit sample: fix stdin checking for flag -2. #102.
    • seqkit rename/split/split2: fix detection of existed outdir.
    • split split: fix bug of seqkit split -i -2 and parallizing it.
    • seqkit version: checking update is optional (-u).
Assets 8
Jan 27, 2020
seqkit: append files from --infile-list to files from CLI argument

@shenwei356 shenwei356 released this Sep 24, 2019 · 166 commits to master since this release

Changes

  • SeqKit v0.11.0 Github Releases (by Release)
    • seqkit: fix hanging when reading from truncated gzip file.
    • new commands:
      • seqkit amplicon: retrieve amplicon (or specific region around it) via primer(s).
    • new commands by @bsipos:
      • seqkit watch: monitoring and online histograms of sequence features.
      • seqkit sana: sanitize broken single line fastq files.
      • seqkit fish: look for short sequences in larger sequences using local alignment.
      • seqkit bam: monitoring and online histograms of BAM record features.
    • seqkit grep/locate: reduce memory occupation when using flag -m/--max-mismatch.
    • seqkit seq: fix panic of computing complement sequence for long sequences containing illegal letters without flag -v on. #84
Assets 8
Pre-release
Pre-release

@shenwei356 shenwei356 released this Aug 21, 2019 · 235 commits to master since this release

Changes

  • seqkit grep/locate: reduce memory occupation when using flag -m/--max-mismatch.
  • new command: seqkit amplicon: retrieve amplicon (or specific region around it) via primer(s)
  • compile with go1.12.9
Assets 5

@shenwei356 shenwei356 released this Jul 30, 2019 · 244 commits to master since this release

Changelog

  • SeqKit v0.10.2
    Github Releases (by Release)
    • seqkit: fix bug of parsing sequence ID delimited by tab (\t). #78
    • seqkit grep: better logic of --delete-matched.
    • seqkit common/rmdup/split: use xxhash to replace MD5 when comparing with sequence, discard flag -m/--md5.
    • seqkit stats: new flag -b/--basename for outputting basename instead of full path.
Assets 8

@shenwei356 shenwei356 released this Feb 27, 2019 · 254 commits to master since this release

Changes

  • SeqKit v0.10.1
    Github Releases (by Release)
    • seqkit fx2tab: new option -q/--avg-qual for outputting average read quality. #60
    • seqkit grep/locate: fix support of X when using -d/--degenerate. #61
    • seqkit translate:
      • new flag -M/--init-codon-as-M to translate initial codon at beginning to 'M'. #62
      • translates --- to - for aligned DNA/RNA, flag -X needed. #63
      • supports codons containing ambiguous bases, e.g., GGN->G, ATH->I. #64
      • new flag -l/--list-transl-table to show details of translate table N
      • new flag -L/--list-transl-table-with-amb-codons to show details of translate table N (including ambigugous codons)
    • seqkit split/split2, fix bug of ignoring -O when reading from stdin.
Assets 8
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