Releases: shenwei356/seqkit
Releases · shenwei356/seqkit
SeqKit v0.13.0
Changes
- SeqKit v0.13.0
seqkit
: fix a rare FASTA/Q parser bug. #127seqkit seq
: output sequence or quality in single line when-s/--seq
or-q/--qual
is on. #132seqkit translate
: delete debug info, #133, and fix typo. #134seqkit split2
: tiny performance improvement. #137seqkit stats
: new flag-i/--stdin-label
for replacing default "-" for stdin. #139seqkit fx2tab
: new flag-s/--seq-hash
for printing hash of sequence (case sensitive). #144seqkit amplicon
:- 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.
- new command
SeqKit v0.12.1
Changes
- SeqKit v0.12.1
seqkit bam
: add colorised and pretty printed output, by @bsipos. #110seqkit locate/grep
: fix bug of-m
, when query contains letters not in subject sequences. #124seqkit split2
: new flag-l/--by-length
for splitting into chunks of N bases.seqkit fx2tab
: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
- do not force switching on
seqkit translate
: supporting multiple frames. #96seqkit 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 defaultindex
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.
- new flag
seqkit rename
: making IDs unique across multiple files, and can write into multiple files. #100seqkit sample
: fix stdin checking for flag-2
. #102.seqkit rename/split/split2
: fix detection of existed outdir.split split
: fix bug ofseqkit 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
). #78seqkit 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. #60seqkit grep/locate
: fix support ofX
when using-d/--degenerate
. #61seqkit 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)
- new flag
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 v0.9.2
Changelog
- SeqKit v0.9.2
seqkit
: stricter checking for value of global flag-t/--seq-type
.seqkit sliding
: fix bug for flag-g/--greedy
. #54seqkit translate
: fix bug for frame < 0. #55seqkit 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