fix test

Author: shenwei356

CHANGELOG.md

@@ -1,4 +1,4 @@
-- [SeqKit v2.1.0](https://github.com/shenwei356/seqkit/releases/tag/v2.1.0) - 2021-08-27
+- [SeqKit v2.1.0](https://github.com/shenwei356/seqkit/releases/tag/v2.1.0) - 2021-11-15
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v2.1.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v2.1.0)
     - `seqkit seq`:
         - **fix filtering by average quality `-Q/-R`**. [#257](https://github.com/shenwei356/seqkit/issues/257)

doc/docs/download.md

@@ -9,13 +9,13 @@ Please cite: **W Shen**, S Le, Y Li\*, F Hu\*. SeqKit: a cross-platform and ultr
 
 OS     |Arch      |File, 中国镜像                                                                                                                                                                                  |Download Count
 :------|:---------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-Linux  |32-bit    |[seqkit_linux_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.0.0/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/v2.0.0/seqkit_linux_386.tar.gz)
-Linux  |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.0.0/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/v2.0.0/seqkit_linux_amd64.tar.gz)
-Linux  |**arm64** |[**seqkit_linux_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.0.0/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/v2.0.0/seqkit_linux_arm64.tar.gz)
-macOS  |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.0.0/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/v2.0.0/seqkit_darwin_amd64.tar.gz)
-macOS  |**arm64** |[**seqkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.0.0/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/v2.0.0/seqkit_darwin_arm64.tar.gz)
-Windows|32-bit    |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.0.0/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/v2.0.0/seqkit_windows_386.exe.tar.gz)
-Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.0.0/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/v2.0.0/seqkit_windows_amd64.exe.tar.gz)
+Linux  |32-bit    |[seqkit_linux_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.1.0/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/v2.1.0/seqkit_linux_386.tar.gz)
+Linux  |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.1.0/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/v2.1.0/seqkit_linux_amd64.tar.gz)
+Linux  |**arm64** |[**seqkit_linux_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.1.0/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/v2.1.0/seqkit_linux_arm64.tar.gz)
+macOS  |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.1.0/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/v2.1.0/seqkit_darwin_amd64.tar.gz)
+macOS  |**arm64** |[**seqkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.1.0/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/v2.1.0/seqkit_darwin_arm64.tar.gz)
+Windows|32-bit    |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.1.0/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/v2.1.0/seqkit_windows_386.exe.tar.gz)
+Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.1.0/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/v2.1.0/seqkit_windows_amd64.exe.tar.gz)
 
 *Notes*
 
@@ -98,6 +98,21 @@ fish:
 
 ## Release History
 
+- [SeqKit v2.1.0](https://github.com/shenwei356/seqkit/releases/tag/v2.1.0) - 2021-11-15
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v2.1.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v2.1.0)
+    - `seqkit seq`:
+        - **fix filtering by average quality `-Q/-R`**. [#257](https://github.com/shenwei356/seqkit/issues/257)
+    - `seqkit convert`:
+        - fix quality encoding checking, change default value of `-N/--thresh-B-in-n-most-common` from `4` to `2`. 
+        [#254](https://github.com/shenwei356/seqkit/issues/254) and [#239](https://github.com/shenwei356/seqkit/issues/239])
+    - `seqkit split`:
+        - fix writing an extra empty file when using `--two-pass`[#244](https://github.com/shenwei356/seqkit/issues/244)
+    - `seqkit subseq`:
+        - fix `--bed` which fail to recognize strand `.`.
+    - `seqkit fq2fa`: 
+        - faster, and do not wrap sequences.
+    - `seqkit grep/locate/mutate`:
+        - detect unquoted comma and show warning message, e.g., `-p 'A{2,}'`. [#250](https://github.com/shenwei356/seqkit/issues/250)
 - [SeqKit v2.0.0](https://github.com/shenwei356/seqkit/releases/tag/v2.0.0) - 2021-08-27
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v2.0.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v2.0.0)
     - **Performance improvements**

go.mod

@@ -17,11 +17,11 @@ require (
 	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 v0.4.0
+	github.com/shenwei356/bio v0.6.0
 	github.com/shenwei356/breader v0.3.1
 	github.com/shenwei356/bwt v0.5.1
 	github.com/shenwei356/go-logging v0.0.0-20171012171522-c6b9702d88ba
-	github.com/shenwei356/util v0.4.0
+	github.com/shenwei356/util v0.5.0
 	github.com/shenwei356/xopen v0.1.0
 	github.com/smallfish/simpleyaml v0.1.0
 	github.com/spf13/cobra v1.2.1
@@ -39,7 +39,6 @@ require (
 	github.com/klauspost/compress v1.13.6 // indirect
 	github.com/mattn/go-runewidth v0.0.13 // indirect
 	github.com/rivo/uniseg v0.2.0 // indirect
-	github.com/shenwei356/bpool v0.0.0-20160710042833-f9e0ee4d0403 // indirect
 	github.com/shenwei356/natsort v0.0.0-20190418160752-600d539c017d // indirect
 	github.com/spf13/pflag v1.0.5 // indirect
 	golang.org/x/crypto v0.0.0-20200622213623-75b288015ac9 // indirect

go.sum

@@ -258,20 +258,19 @@ github.com/rogpeppe/go-internal v1.3.0/go.mod h1:M8bDsm7K2OlrFYOpmOWEs/qY81heoFR
 github.com/russross/blackfriday/v2 v2.0.1/go.mod h1:+Rmxgy9KzJVeS9/2gXHxylqXiyQDYRxCVz55jmeOWTM=
 github.com/ryanuber/columnize v0.0.0-20160712163229-9b3edd62028f/go.mod h1:sm1tb6uqfes/u+d4ooFouqFdy9/2g9QGwK3SQygK0Ts=
 github.com/sean-/seed v0.0.0-20170313163322-e2103e2c3529/go.mod h1:DxrIzT+xaE7yg65j358z/aeFdxmN0P9QXhEzd20vsDc=
-github.com/shenwei356/bio v0.4.0 h1:oY83pyNFGFHTZnkBkTSFjUqm12iFfJ561BhXVoHdL2I=
-github.com/shenwei356/bio v0.4.0/go.mod h1:OTcIoUSG24Ozq/Yln6bh23jEsvOW68OE6XgTihRokQ0=
-github.com/shenwei356/bpool v0.0.0-20160710042833-f9e0ee4d0403 h1:/3JklLnHXiWUBxWc3joQYavDQJpncRhRA909cUb7eOw=
-github.com/shenwei356/bpool v0.0.0-20160710042833-f9e0ee4d0403/go.mod h1:YkgdTWfNnJgv5HVJbVSDmxQtkK3/jZWDoqcG26BVU8k=
+github.com/shenwei356/bio v0.6.0 h1:od1J1/tpXZ5p6DiPa5kCM+ijl1uesSmndhmZkirnglE=
+github.com/shenwei356/bio v0.6.0/go.mod h1:LL8JBeJnKQ4esixngQZiTkZgO1/by1qI0XhMrUl7T8M=
 github.com/shenwei356/breader v0.3.1 h1:OjgfeHhpNGQPkS1+lgsl4eNuuO//Y16N6TkqG5oxO5U=
 github.com/shenwei356/breader v0.3.1/go.mod h1:UR11JJCxU9s7eUdU4xn3L/VodxoXzWhjJPh8WZbb+us=
 github.com/shenwei356/bwt v0.5.1 h1:pq9KxkJPwzUwPjwWqfTOkUmzwHm8JtMkZxBkqkzuIVo=
 github.com/shenwei356/bwt v0.5.1/go.mod h1:V2hX4adhr4WfFpy2ogKiV8A2WO9FeK0wkq1o3/R91mE=
 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/kmers v0.1.0/go.mod h1:23Ltr95n98LYy9OtJMFSzkmU/1nmdYwgzqB3walAQ6g=
 github.com/shenwei356/natsort v0.0.0-20190418160752-600d539c017d h1:eeXLHcXyGEr72V1SOSEI7vSzUOTJvHutwF7Ykm+hscQ=
 github.com/shenwei356/natsort v0.0.0-20190418160752-600d539c017d/go.mod h1:SiiGiRFyRtV7S9RamOrmQR5gpGIRhWJM1w0EtmuQ1io=
-github.com/shenwei356/util v0.4.0 h1:1E7iYZYGqdEXANQgLvayhlUQl4CWaolYZlptyOyH1PQ=
-github.com/shenwei356/util v0.4.0/go.mod h1:kTUqFu3nBscRXmIFdr4Lv3UkAjisrXNCKqp6GrnZTcU=
+github.com/shenwei356/util v0.5.0 h1:gbPuGYVggNLOSORuZLnpaB2DrIpyDFolHiZQkyja+XU=
+github.com/shenwei356/util v0.5.0/go.mod h1:goFN/u2HgvfbOsEgoHA2hUEet+9KjZpRavrVGz9cm30=
 github.com/shenwei356/xopen v0.1.0 h1:PizY52rLA7A6EdkwKZ6A8h8/a+c9DCBXqfLtwVzsWnM=
 github.com/shenwei356/xopen v0.1.0/go.mod h1:6EQUa6I7Zsl2GQKqcL9qGLrTzVE+oZyly+uhzovQYSk=
 github.com/shurcooL/sanitized_anchor_name v1.0.0/go.mod h1:1NzhyTcUVG4SuEtjjoZeVRXNmyL/1OwPU0+IJeTBvfc=
@@ -302,11 +301,13 @@ github.com/twotwotwo/sorts v0.0.0-20160814051341-bf5c1f2b8553 h1:DRC1ubdb3ZmyyIe
 github.com/twotwotwo/sorts v0.0.0-20160814051341-bf5c1f2b8553/go.mod h1:Rj7Csq/tZ/egz+Ltc2IVpsA5309AmSMEswjkTZmq2Xc=
 github.com/ulikunitz/xz v0.5.6/go.mod h1:2bypXElzHzzJZwzH67Y6wb67pO62Rzfn7BSiF4ABRW8=
 github.com/ulikunitz/xz v0.5.10/go.mod h1:nbz6k7qbPmH4IRqmfOplQw/tblSgqTqBwxkY0oWt/14=
+github.com/will-rowe/nthash v0.4.0/go.mod h1:5ezweuK0J5j+/7lih/RkrSmnxI3hoaPpQiVWJ7rd960=
 github.com/yuin/goldmark v1.1.25/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74=
 github.com/yuin/goldmark v1.1.27/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74=
 github.com/yuin/goldmark v1.1.32/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74=
 github.com/yuin/goldmark v1.2.1/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74=
 github.com/yuin/goldmark v1.3.5/go.mod h1:mwnBkeHKe2W/ZEtQ+71ViKU8L12m81fl3OWwC1Zlc8k=
+github.com/zeebo/wyhash v0.0.1/go.mod h1:Ti+OwfNtM5AZiYAL0kOPIfliqDP5c0VtOnnMAqzuuZk=
 go.etcd.io/etcd/api/v3 v3.5.0/go.mod h1:cbVKeC6lCfl7j/8jBhAK6aIYO9XOjdptoxU/nLQcPvs=
 go.etcd.io/etcd/client/pkg/v3 v3.5.0/go.mod h1:IJHfcCEKxYu1Os13ZdwCwIUTUVGYTSAM3YSwc9/Ac1g=
 go.etcd.io/etcd/client/v2 v2.305.0/go.mod h1:h9puh54ZTgAKtEbut2oe9P4L/oqKCVB6xsXlzd7alYQ=

tests/test.sh

@@ -203,7 +203,7 @@ assert_equal $(cat $STDOUT_FILE | md5sum | cut -d" " -f 1) $($app seq $file | md
 
 file=tests/reads_1.fq.gz
 run fq2fa $app fq2fa $file
-assert_equal $(cat $STDOUT_FILE | md5sum | cut -d" " -f 1) $($app fx2tab $file | cut -f 1,2 | $app tab2fx | md5sum | cut -d" " -f 1)
+assert_equal $(cat $STDOUT_FILE | md5sum | cut -d" " -f 1) $($app fx2tab $file | cut -f 1,2 | $app tab2fx -w 0 | md5sum | cut -d" " -f 1)
 
 READS_FQ=tests/pcs109_5k.fq
 NANO_FQ_TSV=tests/pcs109_5k_fq_NanoPlot.tsv