[med-svn] [Git][med-team/seqkit][master] 2 commits: New upstream version 0.16.1+ds

Nilesh Patra (@nilesh) gitlab at salsa.debian.org
Mon Jul 26 22:20:40 BST 2021



Nilesh Patra pushed to branch master at Debian Med / seqkit


Commits:
41351e95 by Nilesh Patra at 2021-07-27T02:50:24+05:30
New upstream version 0.16.1+ds
- - - - -
4bd6a740 by Nilesh Patra at 2021-07-27T02:50:24+05:30
[skip ci] Interim changelog entry

- - - - -


7 changed files:

- CHANGELOG.md
- debian/changelog
- doc/docs/download.md
- seqkit/cmd/pair.go
- seqkit/cmd/shuffle.go
- seqkit/cmd/sort.go
- seqkit/cmd/version.go


Changes:

=====================================
CHANGELOG.md
=====================================
@@ -1,5 +1,7 @@
-
-
+- [SeqKit v0.16.1](https://github.com/shenwei356/seqkit/releases/tag/v0.16.1)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v0.16.1/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v0.16.1)
+    - `seqkit shuffle --two-pass`: fix bug introduced in [#173](https://github.com/shenwei356/seqkit/issues/173) . [#209](https://github.com/shenwei356/seqkit/issues/209)
+    - `seqkit pair`: fix a dangerous bug: when input files are not in current directory, input files were overwritten.
 - [SeqKit v0.16.0](https://github.com/shenwei356/seqkit/releases/tag/v0.16.0)
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v0.16.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v0.16.0)
     - new command `seqkit head-genome`:


=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-seqkit (0.16.0+ds-1) UNRELEASED; urgency=medium
+seqkit (0.16.1+ds-1) UNRELEASED; urgency=medium
 
   * d/watch: Fix watch regex
   * New upstream version 0.16.0+ds


=====================================
doc/docs/download.md
=====================================
@@ -6,28 +6,10 @@ SeqKit is implemented in [Go](https://golang.org/) programming language,
 
 ## Latest Version
 
-- [SeqKit v0.16.0](https://github.com/shenwei356/seqkit/releases/tag/v0.16.0)
-[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v0.16.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v0.16.0)
-    - new command `seqkit head-genome`:
-        - print sequences of the first genome with common prefixes in name
-    - `seqkit grep/locate/amplicon -m`
-        - *much faster (300-400x) searching with mismatch allowed* by optimizing FM-indexing and parallelization.
-        - new flag `-I/--immediate-output`.
-    - `seqkit grep/locate`:
-        - fix bug of `-m` when querying contains letters not in alphabet, usually for protein sequences. [#178](https://github.com/shenwei356/seqkit/issues/178), [#179](https://github.com/shenwei356/seqkit/issues/179)
-        - onply search on positive strand when searching unlimited or protein sequences.
-    - `seqkit locate`:
-        - removing debug info for `-r` introduced in a0f6b6e. [#180](https://github.com/shenwei356/seqkit/issues/180)
-    - `seqkit amplicon`:
-        - fix bug of `-m`, when mismatch is allowed.
-    - `seqkit fx2tab`:
-        - new flag `-C/--base-count` for counting bases. [#183](https://github.com/shenwei356/seqkit/issues/183)
-    -  `seqkit tab2fx`:
-        -  fix a rare bug. [#197](https://github.com/shenwei356/seqkit/issues/197)
-    - `seqkit subseq`:
-        - fix bug for BED with empty columns. [#195](https://github.com/shenwei356/seqkit/issues/195)
-    - `seqkit genautocomplete`: 
-        - **support bash|zsh|fish|powershell**.
+- [SeqKit v0.16.1](https://github.com/shenwei356/seqkit/releases/tag/v0.16.1)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v0.16.1/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v0.16.1)
+    - `seqkit shuffle --two-pass`: fix bug introduced in [#173](https://github.com/shenwei356/seqkit/issues/173) . [#209](https://github.com/shenwei356/seqkit/issues/209)
+    - `seqkit pair`: fix a dangerous bug: when input files are not in current directory, input files were overwritten.
 
 ### Please cite
 
@@ -44,13 +26,13 @@ SeqKit is implemented in [Go](https://golang.org/) programming language,
 
 OS     |Arch      |File, 中国镜像                                                                                                                                                                                  |Download Count
 :------|:---------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-Linux  |32-bit    |[seqkit_linux_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v0.16.0/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/v0.16.0/seqkit_linux_386.tar.gz)
-Linux  |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.16.0/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/v0.16.0/seqkit_linux_amd64.tar.gz)
-Linux  |**arm64** |[**seqkit_linux_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.16.0/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/v0.16.0/seqkit_linux_arm64.tar.gz)
-macOS  |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.16.0/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/v0.16.0/seqkit_darwin_amd64.tar.gz)
-macOS  |**arm64** |[**seqkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.16.0/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/v0.16.0/seqkit_darwin_arm64.tar.gz)
-Windows|32-bit    |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v0.16.0/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/v0.16.0/seqkit_windows_386.exe.tar.gz)
-Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.16.0/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/v0.16.0/seqkit_windows_amd64.exe.tar.gz)
+Linux  |32-bit    |[seqkit_linux_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v0.16.1/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/v0.16.1/seqkit_linux_386.tar.gz)
+Linux  |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.16.1/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/v0.16.1/seqkit_linux_amd64.tar.gz)
+Linux  |**arm64** |[**seqkit_linux_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.16.1/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/v0.16.1/seqkit_linux_arm64.tar.gz)
+macOS  |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.16.1/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/v0.16.1/seqkit_darwin_amd64.tar.gz)
+macOS  |**arm64** |[**seqkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.16.1/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/v0.16.1/seqkit_darwin_arm64.tar.gz)
+Windows|32-bit    |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v0.16.1/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/v0.16.1/seqkit_windows_386.exe.tar.gz)
+Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.16.1/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/v0.16.1/seqkit_windows_amd64.exe.tar.gz)
 
 
 ## Installation
@@ -128,6 +110,28 @@ fish:
 
 ## Release History
 
+- [SeqKit v0.16.0](https://github.com/shenwei356/seqkit/releases/tag/v0.16.0)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v0.16.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v0.16.0)
+    - new command `seqkit head-genome`:
+        - print sequences of the first genome with common prefixes in name
+    - `seqkit grep/locate/amplicon -m`
+        - *much faster (300-400x) searching with mismatch allowed* by optimizing FM-indexing and parallelization.
+        - new flag `-I/--immediate-output`.
+    - `seqkit grep/locate`:
+        - fix bug of `-m` when querying contains letters not in alphabet, usually for protein sequences. [#178](https://github.com/shenwei356/seqkit/issues/178), [#179](https://github.com/shenwei356/seqkit/issues/179)
+        - onply search on positive strand when searching unlimited or protein sequences.
+    - `seqkit locate`:
+        - removing debug info for `-r` introduced in a0f6b6e. [#180](https://github.com/shenwei356/seqkit/issues/180)
+    - `seqkit amplicon`:
+        - fix bug of `-m`, when mismatch is allowed.
+    - `seqkit fx2tab`:
+        - new flag `-C/--base-count` for counting bases. [#183](https://github.com/shenwei356/seqkit/issues/183)
+    -  `seqkit tab2fx`:
+        -  fix a rare bug. [#197](https://github.com/shenwei356/seqkit/issues/197)
+    - `seqkit subseq`:
+        - fix bug for BED with empty columns. [#195](https://github.com/shenwei356/seqkit/issues/195)
+    - `seqkit genautocomplete`: 
+        - **support bash|zsh|fish|powershell**.
 - [SeqKit v0.15.0](https://github.com/shenwei356/seqkit/releases/tag/v0.15.0)
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v0.15.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v0.15.0)
     - `seqkit grep/locate`: update help message.


=====================================
seqkit/cmd/pair.go
=====================================
@@ -86,7 +86,10 @@ Attensions:
 		}
 
 		var addSuffix bool
-		if outdir != "./" && outdir != "." {
+
+		if filepath.Clean(filepath.Dir(read1)) == filepath.Clean(outdir) {
+			addSuffix = true
+		} else if outdir != "./" && outdir != "." {
 			existed, err := pathutil.DirExists(outdir)
 			checkError(err)
 			if existed {
@@ -103,8 +106,6 @@ Attensions:
 			} else {
 				checkError(os.MkdirAll(outdir, 0755))
 			}
-		} else if filepath.Clean(filepath.Dir(read1)) == filepath.Clean(outdir) {
-			addSuffix = true
 		}
 
 		var reader1, reader2 *fastx.Reader


=====================================
seqkit/cmd/shuffle.go
=====================================
@@ -216,6 +216,9 @@ Secondly, seqkit shuffles sequence IDs and extract sequences by FASTA index.
 			sequence := subseqByFaixNotCleaned(faidx, chr, r, 1, -1)
 			outfh.Write([]byte(fmt.Sprintf(">%s\n", chr)))
 			outfh.Write(sequence)
+			if len(sequence) > 0 && sequence[len(sequence)-1] != '\n' {
+				outfh.WriteString("\n")
+			}
 		}
 
 		if (isStdin(file) || !isPlainFile(file)) && !keepTemp {


=====================================
seqkit/cmd/sort.go
=====================================
@@ -399,8 +399,7 @@ and extracts sequences by FASTA index.
 				sequence := subseqByFaixNotCleaned(faidx, chr, r, 1, -1)
 				outfh.Write([]byte(fmt.Sprintf(">%s\n", chr)))
 				outfh.Write(sequence)
-				if len(sequence) > 0 && sequence[len(sequence)-1] == '\n' {
-				} else {
+				if len(sequence) > 0 && sequence[len(sequence)-1] != '\n' {
 					outfh.WriteString("\n")
 				}
 			}
@@ -416,8 +415,7 @@ and extracts sequences by FASTA index.
 				sequence := subseqByFaixNotCleaned(faidx, chr, r, 1, -1)
 				outfh.Write([]byte(fmt.Sprintf(">%s\n", chr)))
 				outfh.Write(sequence)
-				if len(sequence) > 0 && sequence[len(sequence)-1] == '\n' {
-				} else {
+				if len(sequence) > 0 && sequence[len(sequence)-1] != '\n' {
 					outfh.WriteString("\n")
 				}
 			}


=====================================
seqkit/cmd/version.go
=====================================
@@ -29,7 +29,7 @@ import (
 )
 
 // VERSION of seqkit
-const VERSION = "0.16.0"
+const VERSION = "0.16.1"
 
 // versionCmd represents the version command
 var versionCmd = &cobra.Command{



View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/compare/74269afe083ed3110d498bcfc78d8652fcde30f8...4bd6a740e922520d8dc9409695075cae1f6aad46

-- 
View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/compare/74269afe083ed3110d498bcfc78d8652fcde30f8...4bd6a740e922520d8dc9409695075cae1f6aad46
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