[med-svn] [Git][med-team/seqkit][upstream] New upstream version 0.16.1+ds
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Mon Jul 26 22:20:10 BST 2021
Nilesh Patra pushed to branch upstream at Debian Med / seqkit
Commits:
5c64580e by Nilesh Patra at 2021-07-27T02:49:18+05:30
New upstream version 0.16.1+ds
- - - - -
6 changed files:
- CHANGELOG.md
- 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)
+[](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)
[](https://github.com/shenwei356/seqkit/releases/tag/v0.16.0)
- new command `seqkit head-genome`:
=====================================
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)
-[](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)
+[](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) |[](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) |[](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) |[](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) |[](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) |[](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) |[](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)|[](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) |[](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) |[](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) |[](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) |[](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) |[](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) |[](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)|[](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)
+[](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)
[](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/-/commit/5c64580ed98f5074e5ef69c89799a1afdcc65afc
--
View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/commit/5c64580ed98f5074e5ef69c89799a1afdcc65afc
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