Update anchr.rs

wang-q · Jun 22, 2024 · fee7414 · fee7414
1 parent b4ce988
commit fee7414
Showing 1 changed file with 19 additions and 7 deletions.
diff --git a/src/anchr.rs b/src/anchr.rs
@@ -18,23 +18,32 @@ fn main() -> anyhow::Result<()> {
         .subcommand(cmd::dep::make_subcommand())
         .subcommand(cmd::ena::make_subcommand())
         .subcommand(cmd::merge::make_subcommand())
+        .subcommand(cmd::overlap::make_subcommand())
         .subcommand(cmd::paf2ovlp::make_subcommand())
         .subcommand(cmd::quorum::make_subcommand())
         .subcommand(cmd::restrict::make_subcommand())
+        .subcommand(cmd::show2ovlp::make_subcommand())
         .subcommand(cmd::template::make_subcommand())
         .subcommand(cmd::trim::make_subcommand())
         .subcommand(cmd::unitigs::make_subcommand())
         .after_help(
             r###"
 Subcommand groups:
 
+* Dependence
+    * dep check
+    * dep install
+
+* Download
+    * ena
+
 * Overlaps
     * Standalone
-        * paf2ovlp
+        * dazzname
         * show2ovlp
+        * paf2ovlp
         * covered
         * restrict
-        * dazzname
     * Daligner pipelines
         * overlap
         * contained
@@ -46,8 +55,6 @@ Subcommand groups:
 
 * Assembling
     * anchors
-    * dep
-    * ena
     * merge
     * quorum
     * trim
@@ -58,15 +65,20 @@ Subcommand groups:
 
     // Check which subcomamnd the user ran...
     match app.get_matches().subcommand() {
+        // Dependence
+        Some(("dep", sub_matches)) => cmd::dep::execute(sub_matches),
+        // Download
+        Some(("ena", sub_matches)) => cmd::ena::execute(sub_matches),
         // Overlaps - Standalone
-        Some(("covered", sub_matches)) => cmd::covered::execute(sub_matches),
         Some(("dazzname", sub_matches)) => cmd::dazzname::execute(sub_matches),
+        Some(("show2ovlp", sub_matches)) => cmd::show2ovlp::execute(sub_matches),
         Some(("paf2ovlp", sub_matches)) => cmd::paf2ovlp::execute(sub_matches),
+        Some(("covered", sub_matches)) => cmd::covered::execute(sub_matches),
         Some(("restrict", sub_matches)) => cmd::restrict::execute(sub_matches),
+        // Overlaps - Daligner pipelines
+        Some(("overlap", sub_matches)) => cmd::overlap::execute(sub_matches),
         // Assembling
         Some(("anchors", sub_matches)) => cmd::anchors::execute(sub_matches),
-        Some(("dep", sub_matches)) => cmd::dep::execute(sub_matches),
-        Some(("ena", sub_matches)) => cmd::ena::execute(sub_matches),
         Some(("merge", sub_matches)) => cmd::merge::execute(sub_matches),
         Some(("quorum", sub_matches)) => cmd::quorum::execute(sub_matches),
         Some(("template", sub_matches)) => cmd::template::execute(sub_matches),