start of CLI stuff.

not doing anything yet

src/bin/commands/mod.rs

@@ -1,2 +1,3 @@
 pub mod command;
 pub mod demux;
+pub mod trimmer;

src/bin/commands/trimmer.rs

@@ -0,0 +1,58 @@
+use crate::commands::command::Command;
+use anyhow::Result;
+use clap::Parser;
+use log::info;
+use std::fs;
+use std::path::PathBuf;
+
+/// Trimming and overlap correction of paired-end reads
+#[derive(Parser, Debug)]
+#[command(version)]
+pub(crate) struct Trimmer {
+    /// Level of compression to use to compress outputs.
+    #[clap(long, short = 'c', default_value = "5")]
+    compression_level: usize,
+
+    /// Minimum difference in base-quality for one read to correct an overlapping
+    /// base from the other read.
+    #[clap(long, short = 'd', default_value = "15")]
+    overlap_min_bq_delta: usize,
+
+    /// Minimum pair overlap length to attempt correction.
+    #[clap(long, short = 'l', default_value = "50")]
+    overlap_min_len: usize,
+
+    /// Maximum error-rate allowed in the overlap.
+    #[clap(long, short = 'e', default_value = "0.02")]
+    overlap_max_error_rate: f64,
+
+    /// The output directory into which to FASTQs.
+    #[clap(long, short = 'o', required = true)]
+    output: PathBuf,
+
+    /// Fastq file for Read1 and Read2
+    #[clap(required = true, num_args = 2)]
+    fastqs: PathBuf,
+}
+
+impl Trimmer {
+    fn prepare(&self) -> Result<()> {
+        if !self.output.exists() {
+            info!("Output directory {:#?} didn't exist, creating it.", self.output);
+            fs::create_dir_all(&self.output)?;
+        }
+        // see here for pooled writer: https://docs.rs/pooled-writer/0.3.0/pooled_writer/
+        //
+        // and https://github.com/fulcrumgenomics/fqtk/blob/ae91e90ecc86826fc632837bb982798a7e6b6f7a/src/bin/commands/demux.rs#L804
+        // and https://github.com/fulcrumgenomics/fqtk/blob/ae91e90ecc86826fc632837bb982798a7e6b6f7a/src/bin/commands/demux.rs#L850-L851
+        // for reader
+        Ok(())
+    }
+}
+
+impl Command for Trimmer {
+    fn execute(&self) -> Result<()> {
+        self.prepare()?;
+        Ok(())
+    }
+}

src/bin/main.rs

@@ -5,7 +5,7 @@ pub mod commands;
 use anyhow::Result;
 use clap::Parser;
 use commands::command::Command;
-use commands::demux::Demux;
+use commands::{demux::Demux, trimmer::Trimmer};
 use enum_dispatch::enum_dispatch;
 use env_logger::Env;
 
@@ -23,6 +23,7 @@ struct Args {
 #[command(version)]
 enum Subcommand {
     Demux(Demux),
+    Trimmer(Trimmer),
 }
 
 fn main() -> Result<()> {