seq: Change the threshold sequence length for parallelizing complement sequence computation

Author: shenwei356

CHANGELOG.md

@@ -7,6 +7,8 @@
     - `seqkit amplicon`:
         - Fix the speed problem, introduced in v2.7.0. [#439](https://github.com/shenwei356/seqkit/issues/439).
         - Slightly faster by reusing objects.
+    - `seqkit seq`:
+        - Change the threshold sequence length for parallelizing complement sequence computation, 1kb->1Mb.
 - [SeqKit v2.7.0](https://github.com/shenwei356/seqkit/releases/tag/v2.7.0) - 2024-01-31
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v2.7.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v2.7.0)
     - `seqkit`:

go.mod

@@ -20,7 +20,7 @@ require (
 	github.com/mattn/go-isatty v0.0.16
 	github.com/mitchellh/go-homedir v1.1.0
 	github.com/pkg/errors v0.9.1
-	github.com/shenwei356/bio v0.13.1
+	github.com/shenwei356/bio v0.13.3
 	github.com/shenwei356/breader v0.3.2
 	github.com/shenwei356/bwt v0.6.1
 	github.com/shenwei356/go-logging v0.0.0-20171012171522-c6b9702d88ba

go.sum

@@ -123,8 +123,8 @@ github.com/rogpeppe/go-internal v1.9.0/go.mod h1:WtVeX8xhTBvf0smdhujwtBcq4Qrzq/f
 github.com/russross/blackfriday/v2 v2.1.0/go.mod h1:+Rmxgy9KzJVeS9/2gXHxylqXiyQDYRxCVz55jmeOWTM=
 github.com/ruudk/golang-pdf417 v0.0.0-20181029194003-1af4ab5afa58/go.mod h1:6lfFZQK844Gfx8o5WFuvpxWRwnSoipWe/p622j1v06w=
 github.com/ruudk/golang-pdf417 v0.0.0-20201230142125-a7e3863a1245/go.mod h1:pQAZKsJ8yyVxGRWYNEm9oFB8ieLgKFnamEyDmSA0BRk=
-github.com/shenwei356/bio v0.13.1 h1:lj1YJMaRxGfyosoihZSyqtW4fW5219v188AAFmcUWVc=
-github.com/shenwei356/bio v0.13.1/go.mod h1:JjWavkWha/UzK0K7dqTVuzkHEBgGNad9yC1hv0YJrG0=
+github.com/shenwei356/bio v0.13.3 h1:tWspivWisj/kS9RmDv8N0WEovn007jUImk8OdtPYZ38=
+github.com/shenwei356/bio v0.13.3/go.mod h1:5TMT6kpb5lQsa1Uz6nh6PGLtvKi8fQ3SWO2sfiBEOnc=
 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 v0.6.1 h1:BDS1nhhIxiC284OKtLBUgy+U5L/7WrvT/ehOExB/DSA=

seqkit/cmd/seq.go

@@ -58,6 +58,7 @@ var seqCmd = &cobra.Command{
 		outFile := config.OutFile
 		quiet := config.Quiet
 		seq.AlphabetGuessSeqLengthThreshold = config.AlphabetGuessSeqLength
+		seq.ComplementSeqLenThreshold = 1000000
 		runtime.GOMAXPROCS(config.Threads)
 
 		reverse := getFlagBool(cmd, "reverse")