SeqKit v0.13.0

Changes

• SeqKit v0.13.0
  • 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.

SeqKit v0.12.1

Changes

• SeqKit v0.12.1
  • 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.

SeqKit v0.12.0

Changes

• SeqKit v0.12.0
  • 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).

SeqKit v0.11.0

Changes

• SeqKit v0.11.0
  • 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

SeqKit v0.10.2

Changelog

• SeqKit v0.10.2
  
  • 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.

SeqKit v0.10.1

Changes

• SeqKit v0.10.1
  
  • 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.

SeqKit v0.10.0

Changs

• SeqKit v0.10.0
  
  • seqkit: report error when input is directory.
  • new command seqkit mutate: edit sequence (point mutation, insertion, deletion).

SeqKit v0.9.3

Changes

• SeqKit v0.9.3
  • seqkit stats: fix panic for empty file. #57
  • seqkit translate: add flag -x/--allow-unknown-codon to translate unknown codon to X. #56

SeqKit v0.9.2

Changelog

• SeqKit v0.9.2
  
  • seqkit: stricter checking for value of global flag -t/--seq-type.
  • seqkit sliding: fix bug for flag -g/--greedy. #54
  • seqkit translate: fix bug for frame < 0. #55
  • seqkit seq: add TAB to default blank characters (flag -G/--gap-letters), and fix filter result when using flag -g/--remove-gaps along with -m/--min-len or -M/--max-len

SeqKit v0.9.1

Changelog

• SeqKit v0.9.1
  
  • seqkit faidx: fix bug of retrieving subsequence with multiple regions on same sequence. #48
  • seqkit sort/shuffle/split: fix bug when using -2/--two-pass to process .gz files. #52