[med-svn] [Git][med-team/seqkit][upstream] New upstream version 2.3.1+ds
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Sep 29 12:36:26 BST 2022
Andreas Tille pushed to branch upstream at Debian Med / seqkit
Commits:
3aba7d0c by Andreas Tille at 2022-09-29T13:31:35+02:00
New upstream version 2.3.1+ds
- - - - -
7 changed files:
- CHANGELOG.md
- doc/docs/download.md
- go.mod
- go.sum
- seqkit/cmd/faidx.go
- seqkit/cmd/grep.go
- seqkit/cmd/locate.go
Changes:
=====================================
CHANGELOG.md
=====================================
@@ -1,3 +1,8 @@
+- [SeqKit v2.3.1](https://github.com/shenwei356/seqkit/releases/tag/v2.3.1) - 2022-09-22
+[](https://github.com/shenwei356/seqkit/releases/tag/v2.3.1)
+ - `seqkit grep/locate`: fix bug of FMIndex building for empty sequences. [#321](https://github.com/shenwei356/seqkit/issues/321)
+ - `seqkit split2`: fix bug of splitting two FASTA files. [#325](https://github.com/shenwei356/seqkit/issues/325)
+ - `seqkit faidx`: `--id-regexp` works now.
- [SeqKit v2.3.0](https://github.com/shenwei356/seqkit/releases/tag/v2.3.0) - 2022-08-12
[](https://github.com/shenwei356/seqkit/releases/tag/v2.3.0)
- `seqkit grep/rename`:
=====================================
doc/docs/download.md
=====================================
@@ -9,31 +9,24 @@ Please cite: **W Shen**, S Le, Y Li\*, F Hu\*. SeqKit: a cross-platform and ultr
## Current Version
-- [SeqKit v2.3.0](https://github.com/shenwei356/seqkit/releases/tag/v2.3.0) - 2022-08-12
-[](https://github.com/shenwei356/seqkit/releases/tag/v2.3.0)
- - `seqkit grep/rename`:
- - *reduce memory comsumption for a lot of searching patterns, and it's faster*. [#305](https://github.com/shenwei356/seqkit/issues/305)
- - 2X faster `-s/--by-seq`.
- - `seqkit split`
- - fix outputting an empty file when the number of sequence equal to the split size. [#293](https://github.com/shenwei356/seqkit/issues/293)
- - add options to set output file prefix and extention. [#296](https://github.com/shenwei356/seqkit/issues/296)
- - `seqkit split2`
- - reduce memory consumption. [#304](https://github.com/shenwei356/seqkit/issues/304)
- - add options to set output file prefix
- - `seqkit stats`:
- - add GC content. [#294](https://github.com/shenwei356/seqkit/issues/294)
+- [SeqKit v2.3.1](https://github.com/shenwei356/seqkit/releases/tag/v2.3.1) - 2022-09-22
+[](https://github.com/shenwei356/seqkit/releases/tag/v2.3.1)
+ - `seqkit grep/locate`: fix bug of FMIndex building for empty sequences. [#321](https://github.com/shenwei356/seqkit/issues/321)
+ - `seqkit split2`: fix bug of splitting two FASTA files. [#325](https://github.com/shenwei356/seqkit/issues/325)
+ - `seqkit faidx`: `--id-regexp` works now.
+
### 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/v2.3.0/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/v2.3.0/seqkit_linux_386.tar.gz)
-Linux |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.3.0/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/v2.3.0/seqkit_linux_amd64.tar.gz)
-Linux |**arm64** |[**seqkit_linux_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.3.0/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/v2.3.0/seqkit_linux_arm64.tar.gz)
-macOS |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.3.0/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/v2.3.0/seqkit_darwin_amd64.tar.gz)
-macOS |**arm64** |[**seqkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.3.0/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/v2.3.0/seqkit_darwin_arm64.tar.gz)
-Windows|32-bit |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.3.0/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/v2.3.0/seqkit_windows_386.exe.tar.gz)
-Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.3.0/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/v2.3.0/seqkit_windows_amd64.exe.tar.gz)
+Linux |32-bit |[seqkit_linux_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.3.1/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/v2.3.1/seqkit_linux_386.tar.gz)
+Linux |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.3.1/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/v2.3.1/seqkit_linux_amd64.tar.gz)
+Linux |**arm64** |[**seqkit_linux_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.3.1/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/v2.3.1/seqkit_linux_arm64.tar.gz)
+macOS |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.3.1/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/v2.3.1/seqkit_darwin_amd64.tar.gz)
+macOS |**arm64** |[**seqkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.3.1/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/v2.3.1/seqkit_darwin_arm64.tar.gz)
+Windows|32-bit |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.3.1/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/v2.3.1/seqkit_windows_386.exe.tar.gz)
+Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.3.1/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/v2.3.1/seqkit_windows_amd64.exe.tar.gz)
*Notes*
@@ -155,6 +148,20 @@ fish:
## Release history
+
+- [SeqKit v2.3.0](https://github.com/shenwei356/seqkit/releases/tag/v2.3.0) - 2022-08-12
+[](https://github.com/shenwei356/seqkit/releases/tag/v2.3.0)
+ - `seqkit grep/rename`:
+ - *reduce memory comsumption for a lot of searching patterns, and it's faster*. [#305](https://github.com/shenwei356/seqkit/issues/305)
+ - 2X faster `-s/--by-seq`.
+ - `seqkit split`
+ - fix outputting an empty file when the number of sequence equal to the split size. [#293](https://github.com/shenwei356/seqkit/issues/293)
+ - add options to set output file prefix and extention. [#296](https://github.com/shenwei356/seqkit/issues/296)
+ - `seqkit split2`
+ - reduce memory consumption. [#304](https://github.com/shenwei356/seqkit/issues/304)
+ - add options to set output file prefix
+ - `seqkit stats`:
+ - add GC content. [#294](https://github.com/shenwei356/seqkit/issues/294)
- [SeqKit v2.2.0](https://github.com/shenwei356/seqkit/releases/tag/v2.2.0) - 2020-03-14
[](https://github.com/shenwei356/seqkit/releases/tag/v2.2.0)
- `seqkit`:
=====================================
go.mod
=====================================
@@ -11,16 +11,16 @@ require (
github.com/dustin/go-humanize v1.0.0
github.com/fsnotify/fsnotify v1.5.1
github.com/iafan/cwalk v0.0.0-20210125030640-586a8832a711
- github.com/klauspost/compress v1.15.8
+ github.com/klauspost/compress v1.15.10
github.com/klauspost/pgzip v1.2.5
github.com/logrusorgru/aurora v2.0.3+incompatible
github.com/mattn/go-colorable v0.1.11
github.com/mattn/go-isatty v0.0.14
github.com/mitchellh/go-homedir v1.1.0
github.com/pkg/errors v0.9.1
- github.com/shenwei356/bio v0.7.0
+ github.com/shenwei356/bio v0.8.1
github.com/shenwei356/breader v0.3.2
- github.com/shenwei356/bwt v0.6.0
+ github.com/shenwei356/bwt v0.6.1
github.com/shenwei356/go-logging v0.0.0-20171012171522-c6b9702d88ba
github.com/shenwei356/util v0.5.0
github.com/shenwei356/xopen v0.2.2
=====================================
go.sum
=====================================
@@ -40,8 +40,8 @@ github.com/inconshreveable/mousetrap v1.0.0 h1:Z8tu5sraLXCXIcARxBp/8cbvlwVa7Z1NH
github.com/inconshreveable/mousetrap v1.0.0/go.mod h1:PxqpIevigyE2G7u3NXJIT2ANytuPF1OarO4DADm73n8=
github.com/jung-kurt/gofpdf v1.0.3-0.20190309125859-24315acbbda5 h1:PJr+ZMXIecYc1Ey2zucXdR73SMBtgjPgwa31099IMv0=
github.com/jung-kurt/gofpdf v1.0.3-0.20190309125859-24315acbbda5/go.mod h1:7Id9E/uU8ce6rXgefFLlgrJj/GYY22cpxn+r32jIOes=
-github.com/klauspost/compress v1.15.8 h1:JahtItbkWjf2jzm/T+qgMxkP9EMHsqEUA6vCMGmXvhA=
-github.com/klauspost/compress v1.15.8/go.mod h1:PhcZ0MbTNciWF3rruxRgKxI5NkcHHrHUDtV4Yw2GlzU=
+github.com/klauspost/compress v1.15.10 h1:Ai8UzuomSCDw90e1qNMtb15msBXsNpH6gzkkENQNcJo=
+github.com/klauspost/compress v1.15.10/go.mod h1:QPwzmACJjUTFsnSHH934V6woptycfrDDJnH7hvFVbGM=
github.com/klauspost/pgzip v1.2.5 h1:qnWYvvKqedOF2ulHpMG72XQol4ILEJ8k2wwRl/Km8oE=
github.com/klauspost/pgzip v1.2.5/go.mod h1:Ch1tH69qFZu15pkjo5kYi6mth2Zzwzt50oCQKQE9RUs=
github.com/kortschak/utter v0.0.0-20190412033250-50fe362e6560/go.mod h1:oDr41C7kH9wvAikWyFhr6UFr8R7nelpmCF5XR5rL7I8=
@@ -68,12 +68,12 @@ github.com/remyoudompheng/bigfft v0.0.0-20200410134404-eec4a21b6bb0 h1:OdAsTTz6O
github.com/rivo/uniseg v0.2.0 h1:S1pD9weZBuJdFmowNwbpi7BJ8TNftyUImj/0WQi72jY=
github.com/rivo/uniseg v0.2.0/go.mod h1:J6wj4VEh+S6ZtnVlnTBMWIodfgj8LQOQFoIToxlJtxc=
github.com/russross/blackfriday/v2 v2.1.0/go.mod h1:+Rmxgy9KzJVeS9/2gXHxylqXiyQDYRxCVz55jmeOWTM=
-github.com/shenwei356/bio v0.7.0 h1:hj+sZHPhLWuCqSa9sy6g88Si8PvdHAdE+U9ebho7wXs=
-github.com/shenwei356/bio v0.7.0/go.mod h1:VsxsECxbPfi9DA9ZAjKX6K7pEAM0/waDYcwUMmAD/Gg=
+github.com/shenwei356/bio v0.8.1 h1:V9GHoteiXtpX8Wy7jSs1M81TDRBqGju++DCzHJ8aBYY=
+github.com/shenwei356/bio v0.8.1/go.mod h1:neE5KTtMM9fqM41UgzoPUUxhs/sL7Ck1CIeDoYz+nQI=
github.com/shenwei356/breader v0.3.2 h1:GLy2clIMck6FdTwj8WLnmhv0PW/7Pp+Wcx7TVEHG0ks=
github.com/shenwei356/breader v0.3.2/go.mod h1:BimwolkMTIr/O4iX7xXtjEB1z5y39G+8I5Tsm9guC3E=
-github.com/shenwei356/bwt v0.6.0 h1:CENEaKLF8iyxYdnYOM19ETIJLqROhBP/vnEAyrQy5Xo=
-github.com/shenwei356/bwt v0.6.0/go.mod h1:2pciIGqLh9Xl3NhbPHAie69rigG0W7xDa0gVHLT+G7g=
+github.com/shenwei356/bwt v0.6.1 h1:BDS1nhhIxiC284OKtLBUgy+U5L/7WrvT/ehOExB/DSA=
+github.com/shenwei356/bwt v0.6.1/go.mod h1:2pciIGqLh9Xl3NhbPHAie69rigG0W7xDa0gVHLT+G7g=
github.com/shenwei356/go-logging v0.0.0-20171012171522-c6b9702d88ba h1:UvnrxFDPmz7agYX0eQ2JEorTKn1ORnZ9dT5OzbjPvK8=
github.com/shenwei356/go-logging v0.0.0-20171012171522-c6b9702d88ba/go.mod h1:LiqYp/K5yCEWOi7Ux/iOF/kjDxtsdYjOGcKHDbEOXFU=
github.com/shenwei356/natsort v0.0.0-20190418160752-600d539c017d h1:eeXLHcXyGEr72V1SOSEI7vSzUOTJvHutwF7Ykm+hscQ=
=====================================
seqkit/cmd/faidx.go
=====================================
@@ -125,7 +125,7 @@ Examples:
idRegexp = "^(.+)$"
} else {
fileFai = file + ".fai"
- idRegexp = fastx.DefaultIDRegexp
+ idRegexp = config.IDRegexp
}
if fileNotExists(fileFai) {
if !quiet {
@@ -153,7 +153,7 @@ Examples:
id2head := make(map[string]string)
var idRe *regexp.Regexp
if fullHead {
- idRe, _ = regexp.Compile(fastx.DefaultIDRegexp)
+ idRe, _ = regexp.Compile(config.IDRegexp)
}
var id string
for head := range idx {
=====================================
seqkit/cmd/grep.go
=====================================
@@ -417,6 +417,10 @@ Examples:
break
}
+ if len(record.Seq.Seq) == 0 {
+ continue
+ }
+
if checkAlphabet {
if fastxReader.Alphabet() == seq.Unlimit || fastxReader.Alphabet() == seq.Protein {
onlyPositiveStrand = true
@@ -545,6 +549,10 @@ Examples:
break
}
+ if len(record.Seq.Seq) == 0 {
+ continue
+ }
+
if checkAlphabet {
if fastxReader.Alphabet() == seq.Unlimit || fastxReader.Alphabet() == seq.Protein {
onlyPositiveStrand = true
=====================================
seqkit/cmd/locate.go
=====================================
@@ -358,6 +358,10 @@ Attentions:
break
}
+ if len(record.Seq.Seq) == 0 {
+ continue
+ }
+
if checkAlphabet {
if fastxReader.Alphabet() == seq.Unlimit || fastxReader.Alphabet() == seq.Protein {
_onlyPositiveStrand = true
@@ -606,6 +610,10 @@ Attentions:
break
}
+ if len(record.Seq.Seq) == 0 {
+ continue
+ }
+
if checkAlphabet {
if fastxReader.Alphabet() == seq.Unlimit || fastxReader.Alphabet() == seq.Protein {
_onlyPositiveStrand = true
View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/commit/3aba7d0c2bf1e8dfa8d5bd853e010e90aaa0548c
--
View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/commit/3aba7d0c2bf1e8dfa8d5bd853e010e90aaa0548c
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