v2.8.0

Author: shenwei356

doc/docs/download.md

@@ -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*
@@ -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`:

doc/docs/usage.md

@@ -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 <shenwei356@gmail.com>
 

seqkit/cmd/version.go

@@ -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{