v2.9.0

Author: shenwei356

CHANGELOG.md

@@ -1,4 +1,4 @@
-- [SeqKit v2.9.0](https://github.com/shenwei356/seqkit/releases/tag/v2.9.0) - 2024-07-xx
+- [SeqKit v2.9.0](https://github.com/shenwei356/seqkit/releases/tag/v2.9.0) - 2024-11-01
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v2.9.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v2.9.0)
     - `seqkit`:
         - **Fix sequence ID parsing with the default regular expression (in this case, we actually use bytes.Index instead) for a rare case: "xxx\tyyy zzz" was wrongly parsed as "xxx\tyyy"**. [#486](https://github.com/shenwei356/seqkit/issues/486)

doc/docs/download.md

@@ -13,14 +13,17 @@ Please cite:
 
 ## Current Version
 
-- [SeqKit v2.8.2](https://github.com/shenwei356/seqkit/releases/tag/v2.8.2) - 2024-05-17
-[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v2.8.2/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v2.8.2)
-    - `seqkit amplicon`:
-        - Fix a big introduced in v2.7.0. When more than one pairs of primers are given, only the last one is used. [#457](https://github.com/shenwei356/seqkit/issues/457)
-    - `seqkit translate`:
-        - Add option `-e/--skip-translate-errors` to skip translate error and output empty sequence. [#458](https://github.com/shenwei356/seqkit/pull/458)
-    - `seqkit split`:
-        - Add flag `-I/--ignore-case` for `-i/--by-id`. [#462](https://github.com/shenwei356/seqkit/issues/462)
+- [SeqKit v2.9.0](https://github.com/shenwei356/seqkit/releases/tag/v2.9.0) - 2024-11-01
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v2.9.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v2.9.0)
+    - `seqkit`:
+        - **Fix sequence ID parsing with the default regular expression (in this case, we actually use bytes.Index instead) for a rare case: "xxx\tyyy zzz" was wrongly parsed as "xxx\tyyy"**. [#486](https://github.com/shenwei356/seqkit/issues/486)
+    - `seqkit locate`:
+        - **Fix `-G/--non-greedy` for tandem repeats**, e.g., ATTCGATTCGATTCG (ATTCGx3).
+    - `seqkit grep/subseq`:
+        - Fix negative regions longer than sequence length. [#479](https://github.com/shenwei356/seqkit/issues/479).
+    - `seqkit stats`:
+        - Add an extra column `sum_n` to count the number of ambiguous characters. [#490](https://github.com/shenwei356/seqkit/issues/490)
+
 
 
 
@@ -29,13 +32,13 @@ Please cite:
 
 OS     |Arch      |File, 中国镜像                                                                                                                                                                                  |Download Count
 :------|:---------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-Linux  |32-bit    |[seqkit_linux_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.8.2/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/v2.8.2/seqkit_linux_386.tar.gz)
-Linux  |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.8.2/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/v2.8.2/seqkit_linux_amd64.tar.gz)
-Linux  |**arm64** |[**seqkit_linux_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.8.2/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/v2.8.2/seqkit_linux_arm64.tar.gz)
-macOS  |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.8.2/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/v2.8.2/seqkit_darwin_amd64.tar.gz)
-macOS  |**arm64** |[**seqkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.8.2/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/v2.8.2/seqkit_darwin_arm64.tar.gz)
-Windows|32-bit    |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.8.2/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/v2.8.2/seqkit_windows_386.exe.tar.gz)
-Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.8.2/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/v2.8.2/seqkit_windows_amd64.exe.tar.gz)
+Linux  |32-bit    |[seqkit_linux_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/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/v2.9.0/seqkit_linux_386.tar.gz)
+Linux  |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/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/v2.9.0/seqkit_linux_amd64.tar.gz)
+Linux  |**arm64** |[**seqkit_linux_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/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/v2.9.0/seqkit_linux_arm64.tar.gz)
+macOS  |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/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/v2.9.0/seqkit_darwin_amd64.tar.gz)
+macOS  |**arm64** |[**seqkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/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/v2.9.0/seqkit_darwin_arm64.tar.gz)
+Windows|32-bit    |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/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/v2.9.0/seqkit_windows_386.exe.tar.gz)
+Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/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/v2.9.0/seqkit_windows_amd64.exe.tar.gz)
 
 
 *Notes*
@@ -157,6 +160,14 @@ fish:
 
 ## Release history
 
+- [SeqKit v2.8.2](https://github.com/shenwei356/seqkit/releases/tag/v2.8.2) - 2024-05-17
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v2.8.2/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v2.8.2)
+    - `seqkit amplicon`:
+        - Fix a big introduced in v2.7.0. When more than one pairs of primers are given, only the last one is used. [#457](https://github.com/shenwei356/seqkit/issues/457)
+    - `seqkit translate`:
+        - Add option `-e/--skip-translate-errors` to skip translate error and output empty sequence. [#458](https://github.com/shenwei356/seqkit/pull/458)
+    - `seqkit split`:
+        - Add flag `-I/--ignore-case` for `-i/--by-id`. [#462](https://github.com/shenwei356/seqkit/issues/462)
 - [SeqKit v2.8.1](https://github.com/shenwei356/seqkit/releases/tag/v2.8.1) - 2024-04-07
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v2.8.1/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v2.8.1)
     - `seqkit sana`:

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: 2.8.0
+Version: 2.9.0
 
 Author: Wei Shen <shenwei356@gmail.com>
 

seqkit/cmd/version.go

@@ -29,7 +29,7 @@ import (
 )
 
 // VERSION of seqkit
-const VERSION = "2.8.2"
+const VERSION = "2.9.0"
 
 // versionCmd represents the version command
 var versionCmd = &cobra.Command{

seqkit/packaging.sh

@@ -17,3 +17,5 @@ for f in seqkit_*; do
     rm -rf $f;
     cd ..;
 done;
+
+ls binaries/*.tar.gz | rush 'cd {/}; md5sum {%} > {%}.md5.txt'