Add initial working CLI for uniwig #1

genimtools/src/main.rs

@@ -4,7 +4,7 @@ use clap::Command;
 use genimtools::tokenizers;
 use genimtools::tools;
 use genimtools::vocab;
-// use genimtools::uniwig;
+use genimtools::uniwig;
 
 pub mod consts {
     pub const VERSION: &str = env!("CARGO_PKG_VERSION");
@@ -23,6 +23,7 @@ fn build_parser() -> Command {
         .subcommand(vocab::cli::make_prune_cli())
         .subcommand(tokenizers::cli::make_tokenization_cli())
         .subcommand(tools::cli::make_tools_cli())
+        .subcommand(uniwig::cli::create_uniwig_cli())
 }
 
 fn main() {
@@ -39,6 +40,9 @@ fn main() {
         Some((tools::consts::TOOLS_CMD, matches)) => {
             let _ = tools::cli::handlers::tools_handler(matches);
         }
+        Some((uniwig::consts::UNIWIG_CMD, matches)) => {
+            uniwig::run_uniwig(matches);
+        }
 
         _ => unreachable!("Subcommand not found"),
     };

genimtools/src/uniwig/README.md

@@ -0,0 +1,14 @@
+# Current Manual testing
+
+Full command:
+```
+cargo run uniwig
+```
+
+# Uniwig
+
+Given a set of bed files, we want to produce 2 [BigWig](http://genome.ucsc.edu/goldenPath/help/bigWig.html) files: one track of the start coordinates, one track of the end coordinates, and one track for core coordinates.
+
+# Usage
+
+CLI or Python Bindings

genimtools/src/uniwig/cli.rs

@@ -0,0 +1,17 @@
+use clap::{Arg, Command};
+
+use crate::uniwig::consts::UNIWIG_CMD;
+
+pub fn create_uniwig_cli() -> Command {
+    Command::new(UNIWIG_CMD)
+        .author("DRC")
+        .about("Given a set of bed files, we want to produce 2")
+        .arg(
+            Arg::new("sorted")
+                .long("sorted")
+                .short('s')
+                .help("Specify if the provided bed file is already sorted by the chromosome number.")
+                .required(false)
+        )
+
+}

genimtools/src/uniwig/mod.rs

@@ -1,3 +1,12 @@
-pub fn run_uniwig() {
-    println!("Im running.")
+use clap::ArgMatches;
+
+pub mod cli;
+
+pub fn run_uniwig(matches: &ArgMatches) {
+    println!("Im running. Here are the arguments: {:?}", matches)
 }
+
+pub mod consts {
+    pub const UNIWIG_CMD: &str = "uniwig";
+
+}