Skip to content

Commit

Permalink
v2.8.0
Browse files Browse the repository at this point in the history
  • Loading branch information
@shenwei356
shenwei356 committed Mar 11, 2024
1 parent 0c6b62e commit 8a37c92
Show file tree
Hide file tree
Showing 3 changed files with 33 additions and 24 deletions.
53 changes: 31 additions & 22 deletions doc/docs/download.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,34 +9,29 @@ Please cite: **W Shen**, S Le, Y Li\*, F Hu\*. SeqKit: a cross-platform and ultr

## Current Version

- [SeqKit v2.7.0](https://github.com/shenwei356/seqkit/releases/tag/v2.7.0) - 2024-01-31
[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v2.7.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v2.7.0)
- `seqkit`:
- Grouping subcommands in help message, which is intuitive for beginners.
- `seqkit grep`:
- New flag: `-D/--allow-duplicated-patterns` for outputting records multiple times when duplicated patterns are given. [#427](https://github.com/shenwei356/seqkit/issues/427)
- `seqkit subseq`:
- Use the ID regular expression from the option `--id-regexp` to create FASTA index file. This solves the panic happened for sequences containing tabs in the headers. [#432](https://github.com/shenwei356/seqkit/issues/432)
- `seqkit split/sort/shuffle`:
- When using the two-pass mode (`-2/--two-pass`), replace possible tabs in the sequence header.
- `seqkit rmdup`:
- Write an empty file of duplicate numbers and lists of IDs even if there's no duplicates when using `-D/--dup-num-file`. [#436](https://github.com/shenwei356/seqkit/issues/436)
- [SeqKit v2.8.0](https://github.com/shenwei356/seqkit/releases/tag/v2.8.0) - 2024-03-11
[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v2.8.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v2.8.0)
- `seqkit stats`:
- New flag `-S/--skip-file-check` to skip input file checking when given files or a file list. It's very useful if you run it with millions of files.


- Add column `N50_num`, an alias of L50, [#15](https://github.com/shenwei356/seqkit/issues/15).
- `seqkit seq/locate/fish/watch`:
- Removing the flag `-V/--validate-seq-length`. Now the whole sequence will be checked if `-v/--validate-seq` is given.
- `seqkit amplicon`:
- Fix the speed problem, introduced in v2.7.0. [#439](https://github.com/shenwei356/seqkit/issues/439).
- Slightly faster by reusing objects.
- `seqkit seq`:
- Change the threshold sequence length for parallelizing complement sequence computation, 1kb->1Mb.

### Links

OS |Arch |File, 中国镜像 |Download Count
:------|:---------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Linux |32-bit |[seqkit_linux_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_linux_386.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_linux_386.tar.gz) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_386.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_linux_386.tar.gz)
Linux |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_linux_amd64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_linux_amd64.tar.gz) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_linux_amd64.tar.gz)
Linux |**arm64** |[**seqkit_linux_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_linux_arm64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_linux_arm64.tar.gz) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_linux_arm64.tar.gz)
macOS |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_darwin_amd64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_darwin_amd64.tar.gz) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_darwin_amd64.tar.gz)
macOS |**arm64** |[**seqkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_darwin_arm64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_darwin_arm64.tar.gz) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_darwin_arm64.tar.gz)
Windows|32-bit |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_windows_386.exe.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_windows_386.exe.tar.gz) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_386.exe.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_windows_386.exe.tar.gz)
Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_windows_amd64.exe.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_windows_amd64.exe.tar.gz)|[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_amd64.exe.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_windows_amd64.exe.tar.gz)
Linux |32-bit |[seqkit_linux_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_linux_386.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_linux_386.tar.gz) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_386.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_linux_386.tar.gz)
Linux |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_linux_amd64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_linux_amd64.tar.gz) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_linux_amd64.tar.gz)
Linux |**arm64** |[**seqkit_linux_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_linux_arm64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_linux_arm64.tar.gz) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_linux_arm64.tar.gz)
macOS |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_darwin_amd64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_darwin_amd64.tar.gz) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_darwin_amd64.tar.gz)
macOS |**arm64** |[**seqkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_darwin_arm64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_darwin_arm64.tar.gz) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_darwin_arm64.tar.gz)
Windows|32-bit |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_windows_386.exe.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_windows_386.exe.tar.gz) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_386.exe.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_windows_386.exe.tar.gz)
Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_windows_amd64.exe.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_windows_amd64.exe.tar.gz)|[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_amd64.exe.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_windows_amd64.exe.tar.gz)


*Notes*
Expand Down Expand Up @@ -158,6 +153,20 @@ fish:

## Release history

- [SeqKit v2.7.0](https://github.com/shenwei356/seqkit/releases/tag/v2.7.0) - 2024-01-31
[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v2.7.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v2.7.0)
- `seqkit`:
- Grouping subcommands in help message, which is intuitive for beginners.
- `seqkit grep`:
- New flag: `-D/--allow-duplicated-patterns` for outputting records multiple times when duplicated patterns are given. [#427](https://github.com/shenwei356/seqkit/issues/427)
- `seqkit subseq`:
- Use the ID regular expression from the option `--id-regexp` to create FASTA index file. This solves the panic happened for sequences containing tabs in the headers. [#432](https://github.com/shenwei356/seqkit/issues/432)
- `seqkit split/sort/shuffle`:
- When using the two-pass mode (`-2/--two-pass`), replace possible tabs in the sequence header.
- `seqkit rmdup`:
- Write an empty file of duplicate numbers and lists of IDs even if there's no duplicates when using `-D/--dup-num-file`. [#436](https://github.com/shenwei356/seqkit/issues/436)
- `seqkit stats`:
- New flag `-S/--skip-file-check` to skip input file checking when given files or a file list. It's very useful if you run it with millions of files.
- [SeqKit v2.6.1](https://github.com/shenwei356/seqkit/releases/tag/v2.6.1) - 2023-11-18
[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v2.6.1/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v2.6.1)
- `seqkit`:
Expand Down
2 changes: 1 addition & 1 deletion doc/docs/usage.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -158,7 +158,7 @@ reproduced in different environments with same random seed.
``` text
SeqKit -- a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Version: 2.7.0
Version: 2.8.0
Author: Wei Shen <[email protected]>
Expand Down
2 changes: 1 addition & 1 deletion seqkit/cmd/version.go
View file
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ import (
)

// VERSION of seqkit
const VERSION = "2.7.1"
const VERSION = "2.8.0"

// versionCmd represents the version command
var versionCmd = &cobra.Command{
Expand Down

0 comments on commit 8a37c92

Please sign in to comment.