v0.9.4

shenwei356 · Sep 18, 2023 · 3e229ef · 3e229ef
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,9 +1,9 @@
 # Changelog
 
-### v0.9.4 - 2023-07-16
+### v0.9.4 - 2023-09-18
 
 - `kmcp merge`:
-    - trim tailing tab in merged result, download results are not affected. [#38](https://github.com/shenwei356/kmcp/issues/38)
+    - trim tailing tab in merged result, down-stream results are not affected. [#38](https://github.com/shenwei356/kmcp/issues/38)
 - `kmcp profile`:
     - fix log of "xx% (yy/zz) reads matched", the numerator should be the number of matched reads instead of reads belonging to references.
     - early quit when no target detected.

diff --git a/docs/download.md b/docs/download.md
@@ -17,37 +17,25 @@ ARM architecture is supported, but `kmcp search` would be slower.
 
 ## Current Version
 
-### [v0.9.3](https://github.com/shenwei356/kmcp/releases/tag/v0.9.3) - 2023-07-16 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/kmcp/v0.9.3/total.svg)](https://github.com/shenwei356/kmcp/releases/tag/v0.9.3)
-
-- `kmcp compute/split-genomes`:
-    - fix a bug in chunk computation when splitting circular genomes (`--circular`).
-- `kmcp search/merge`:
-    - append simple stats to the search result as comment lines, including the number of input and matched queries. e.g.,
-
-            # input queries: 930254
-            # matched queries: 923820
-            # matched percentage: 99.3084%
+### [v0.9.4](https://github.com/shenwei356/kmcp/releases/tag/v0.9.4) - 2023-09-18 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/kmcp/v0.9.4/total.svg)](https://github.com/shenwei356/kmcp/releases/tag/v0.9.4)
 
+- `kmcp merge`:
+    - trim tailing tab in merged result, down-stream results are not affected. [#38](https://github.com/shenwei356/kmcp/issues/38)
 - `kmcp profile`:
-    - fix metaphlan out format. [#34](https://github.com/shenwei356/kmcp/issues/34)
-    - show stats of the number of input and matched queries in log. **It would be helpful to show whether the reference genomes cover all microorganisms in the sample**.
-
-            20:00:55.295 [INFO] 99.3084% (923820/930254) reads matched
-            20:00:55.295 [INFO] 100.0000% (923820/923820) matched reads belong to the 2 references in the profile
+    - fix log of "xx% (yy/zz) reads matched", the numerator should be the number of matched reads instead of reads belonging to references.
+    - early quit when no target detected.
+    - slightly speedup.
 
-- new tutorials:
-    - [Detecting specific pathogens](https://bioinf.shenwei.me/kmcp/tutorial/detecting-pathogens)
-    - [Detecting contaminated sequences](https://bioinf.shenwei.me/kmcp/tutorial/detecting-contaminated-seqs)
 
 ### Links
 
 OS     |Arch      |File, 中国镜像                                                                                                                                                                                  |Download Count
 :------|:---------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-Linux  |**64-bit**|[**kmcp_linux_amd64.tar.gz**](https://github.com/shenwei356/kmcp/releases/download/v0.9.3/kmcp_linux_amd64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/kmcp/kmcp_linux_amd64.tar.gz)                  |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/kmcp/latest/kmcp_linux_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/kmcp/releases/download/v0.9.3/kmcp_linux_amd64.tar.gz)
-Linux  |arm64     |[**kmcp_linux_arm64.tar.gz**](https://github.com/shenwei356/kmcp/releases/download/v0.9.3/kmcp_linux_arm64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/kmcp/kmcp_linux_arm64.tar.gz)                  |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/kmcp/latest/kmcp_linux_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/kmcp/releases/download/v0.9.3/kmcp_linux_arm64.tar.gz)
-macOS  |**64-bit**|[**kmcp_darwin_amd64.tar.gz**](https://github.com/shenwei356/kmcp/releases/download/v0.9.3/kmcp_darwin_amd64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/kmcp/kmcp_darwin_amd64.tar.gz)               |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/kmcp/latest/kmcp_darwin_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/kmcp/releases/download/v0.9.3/kmcp_darwin_amd64.tar.gz)
-macOS  |arm64     |[**kmcp_darwin_arm64.tar.gz**](https://github.com/shenwei356/kmcp/releases/download/v0.9.3/kmcp_darwin_arm64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/kmcp/kmcp_darwin_arm64.tar.gz)               |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/kmcp/latest/kmcp_darwin_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/kmcp/releases/download/v0.9.3/kmcp_darwin_arm64.tar.gz)
-Windows|**64-bit**|[**kmcp_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/kmcp/releases/download/v0.9.3/kmcp_windows_amd64.exe.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/kmcp/kmcp_windows_amd64.exe.tar.gz)|[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/kmcp/latest/kmcp_windows_amd64.exe.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/kmcp/releases/download/v0.9.3/kmcp_windows_amd64.exe.tar.gz)
+Linux  |**64-bit**|[**kmcp_linux_amd64.tar.gz**](https://github.com/shenwei356/kmcp/releases/download/v0.9.4/kmcp_linux_amd64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/kmcp/kmcp_linux_amd64.tar.gz)                  |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/kmcp/latest/kmcp_linux_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/kmcp/releases/download/v0.9.4/kmcp_linux_amd64.tar.gz)
+Linux  |arm64     |[**kmcp_linux_arm64.tar.gz**](https://github.com/shenwei356/kmcp/releases/download/v0.9.4/kmcp_linux_arm64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/kmcp/kmcp_linux_arm64.tar.gz)                  |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/kmcp/latest/kmcp_linux_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/kmcp/releases/download/v0.9.4/kmcp_linux_arm64.tar.gz)
+macOS  |**64-bit**|[**kmcp_darwin_amd64.tar.gz**](https://github.com/shenwei356/kmcp/releases/download/v0.9.4/kmcp_darwin_amd64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/kmcp/kmcp_darwin_amd64.tar.gz)               |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/kmcp/latest/kmcp_darwin_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/kmcp/releases/download/v0.9.4/kmcp_darwin_amd64.tar.gz)
+macOS  |arm64     |[**kmcp_darwin_arm64.tar.gz**](https://github.com/shenwei356/kmcp/releases/download/v0.9.4/kmcp_darwin_arm64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/kmcp/kmcp_darwin_arm64.tar.gz)               |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/kmcp/latest/kmcp_darwin_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/kmcp/releases/download/v0.9.4/kmcp_darwin_arm64.tar.gz)
+Windows|**64-bit**|[**kmcp_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/kmcp/releases/download/v0.9.4/kmcp_windows_amd64.exe.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/kmcp/kmcp_windows_amd64.exe.tar.gz)|[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/kmcp/latest/kmcp_windows_amd64.exe.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/kmcp/releases/download/v0.9.4/kmcp_windows_amd64.exe.tar.gz)
 
 *Notes:*
 
@@ -148,6 +136,28 @@ fish:
 
 ## Release History
 
+### [v0.9.3](https://github.com/shenwei356/kmcp/releases/tag/v0.9.3) - 2023-07-16 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/kmcp/v0.9.3/total.svg)](https://github.com/shenwei356/kmcp/releases/tag/v0.9.3)
+
+- `kmcp compute/split-genomes`:
+    - fix a bug in chunk computation when splitting circular genomes (`--circular`).
+- `kmcp search/merge`:
+    - append simple stats to the search result as comment lines, including the number of input and matched queries. e.g.,
+
+            # input queries: 930254
+            # matched queries: 923820
+            # matched percentage: 99.3084%
+
+- `kmcp profile`:
+    - fix metaphlan out format. [#34](https://github.com/shenwei356/kmcp/issues/34)
+    - show stats of the number of input and matched queries in log. **It would be helpful to show whether the reference genomes cover all microorganisms in the sample**.
+
+            20:00:55.295 [INFO] 99.3084% (923820/930254) reads matched
+            20:00:55.295 [INFO] 100.0000% (923820/923820) matched reads belong to the 2 references in the profile
+
+- new tutorials:
+    - [Detecting specific pathogens](https://bioinf.shenwei.me/kmcp/tutorial/detecting-pathogens)
+    - [Detecting contaminated sequences](https://bioinf.shenwei.me/kmcp/tutorial/detecting-contaminated-seqs)
+
 ### [v0.9.2](https://github.com/shenwei356/kmcp/releases/tag/v0.9.2) - 2023-05-16 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/kmcp/v0.9.2/total.svg)](https://github.com/shenwei356/kmcp/releases/tag/v0.9.2)
 
 - `kmcp profile/cos2simi/filter/index-info/merge-regions/query-fpr`:

diff --git a/docs/usage.md b/docs/usage.md
@@ -26,7 +26,7 @@ KMCP is a command-line tool consisting of several subcommands.
 ```text
 
     Program: kmcp (K-mer-based Metagenomic Classification and Profiling)
-    Version: v0.9.2
+    Version: v0.9.4
   Documents: https://bioinf.shenwei.me/kmcp
 Source code: https://github.com/shenwei356/kmcp