v0.1.0. LexicMap only does mapping

CHANGELOG.md

@@ -1,3 +1,7 @@
 # Changelog
 
-### v0.0.1 - 2023-11-19
+### v0.1.0 - 2024-01-15
+
+- The first release.
+- Seed indexing and quering are performed in RAM.
+- GTDB r214 with 10k masks: index size 75GB, RAM: 130GB.

README.md

@@ -1,6 +1,6 @@
 ## LexicMap
 
-LexicHash-based long-read mapping and metagenomic profiling.
+LexicMap: fast sequence alignment against millions of microbial genomes​.
 
 ## Support
 

go.mod

@@ -12,7 +12,7 @@ require (
 	github.com/pkg/errors v0.9.1
 	github.com/shenwei356/bio v0.12.0
 	github.com/shenwei356/go-logging v0.0.0-20171012171522-c6b9702d88ba
-	github.com/shenwei356/lexichash v0.0.0-00010101000000-000000000000
+	github.com/shenwei356/lexichash v0.1.0
 	github.com/shenwei356/util v0.5.2
 	github.com/spf13/cobra v1.8.0
 	github.com/twotwotwo/sorts v0.0.0-20160814051341-bf5c1f2b8553

lexicmap/cmd/root.go

@@ -31,9 +31,9 @@ import (
 // RootCmd represents the base command when called without any subcommands
 var RootCmd = &cobra.Command{
 	Use:   "lexicmap",
-	Short: "LexicHash-based long-read mapping and metagenomic profiling",
+	Short: "efficient sequence alignment against millions of microbial genomes​",
 	Long: fmt.Sprintf(`
-    Program: LexicMap: LexicHash-based long-read mapping and metagenomic profiling
+    Program: LexicMap: efficient sequence alignment against millions of microbial genomes
     Version: v%s
   Documents: https://bioinf.shenwei.me/LexicMap
 Source code: https://github.com/shenwei356/LexicMap
@@ -87,10 +87,16 @@ Aliases:
   {{.NameAndAliases}}{{end}}{{if .HasExample}}
 
 Examples:
-{{.Example}}{{end}}{{if .HasAvailableSubCommands}}
+{{.Example}}{{end}}{{if .HasAvailableSubCommands}}{{$cmds := .Commands}}{{if eq (len .Groups) 0}}
 
-Available Commands:{{range .Commands}}{{if (or .IsAvailableCommand (eq .Name "help"))}}
-  {{rpad .Name .NamePadding }} {{.Short}}{{end}}{{end}}{{end}}{{if .HasAvailableLocalFlags}}
+Available Commands:{{range $cmds}}{{if (or .IsAvailableCommand (eq .Name "help"))}}
+  {{rpad .Name .NamePadding }} {{.Short}}{{end}}{{end}}{{else}}{{range $group := .Groups}}
+
+{{.Title}}{{range $cmds}}{{if (and (eq .GroupID $group.ID) (or .IsAvailableCommand (eq .Name "help")))}}
+  {{rpad .Name .NamePadding }} {{.Short}}{{end}}{{end}}{{end}}{{if not .AllChildCommandsHaveGroup}}
+
+Additional Commands:{{range $cmds}}{{if (and (eq .GroupID "") (or .IsAvailableCommand (eq .Name "help")))}}
+  {{rpad .Name .NamePadding }} {{.Short}}{{end}}{{end}}{{end}}{{end}}{{end}}{{if .HasAvailableLocalFlags}}
 
 Flags:
 {{.LocalFlags.FlagUsagesWrapped 110 | trimTrailingWhitespaces}}{{end}}{{if .HasAvailableInheritedFlags}}

lexicmap/cmd/version.go

@@ -30,7 +30,7 @@ import (
 )
 
 // VERSION is the version
-var VERSION = "0.0.2"
+var VERSION = "0.1.0"
 
 // versionCmd represents the version command
 var versionCmd = &cobra.Command{