move more options into structs

src/cellfilter.rs

@@ -11,6 +11,7 @@ use anyhow::{anyhow, Context};
 use slog::crit;
 use slog::info;
 
+use crate::prog_opts::GenPermitListOpts;
 use crate::utils as afutils;
 #[allow(unused_imports)]
 use ahash::{AHasher, RandomState};
@@ -30,6 +31,7 @@ use std::io::{BufRead, BufReader, Read};
 use std::io::{BufWriter, Write};
 use std::time::Instant;
 
+#[derive(Debug)]
 pub enum CellFilterMethod {
     // cut off at this cell in
     // the frequency sorted list
@@ -580,20 +582,16 @@ fn process_filtered(
 /// (i.e. "permitted") barcode values, as well as
 /// a map from each correctable barcode to the
 /// permitted barcode to which it maps.
-#[allow(clippy::too_many_arguments)]
-pub fn generate_permit_list(
-    rad_dir: String,
-    output_dir: String,
-    filter_meth: CellFilterMethod,
-    expected_ori: Strand,
-    version: &str,
-    velo_mode: bool,
-    cmdline: &str,
-    //top_k: Option<usize>,
-    //valid_bc_file: Option<String>,
-    //use_knee_distance: bool,
-    log: &slog::Logger,
-) -> anyhow::Result<u64> {
+pub fn generate_permit_list(gpl_opts: GenPermitListOpts) -> anyhow::Result<u64> {
+    let rad_dir = gpl_opts.input_dir;
+    let output_dir = gpl_opts.output_dir;
+    let filter_meth = gpl_opts.fmeth;
+    let expected_ori = gpl_opts.expected_ori;
+    let version = gpl_opts.version;
+    let velo_mode = gpl_opts.velo_mode;
+    let cmdline = gpl_opts.cmdline;
+    let log = gpl_opts.log;
+
     let i_dir = std::path::Path::new(&rad_dir);
 
     if !i_dir.exists() {

src/main.rs

@@ -19,7 +19,7 @@ use slog::{crit, o, warn, Drain};
 use std::path::Path;
 
 use alevin_fry::cellfilter::{generate_permit_list, CellFilterMethod};
-use alevin_fry::prog_opts::QuantOpts;
+use alevin_fry::prog_opts::{GenPermitListOpts, QuantOpts};
 use alevin_fry::quant::{ResolutionStrategy, SplicedAmbiguityModel};
 
 #[global_allocator]
@@ -336,16 +336,18 @@ fn main() -> anyhow::Result<()> {
         // velo_mode --- currently, on this branch, it is always false
         let velo_mode = false; //t.is_present("velocity-mode");
 
-        match generate_permit_list(
-            input_dir,
-            output_dir,
-            fmeth,
-            expected_ori,
-            VERSION,
-            velo_mode,
-            &cmdline,
-            &log,
-        ) {
+        let gpl_opts = GenPermitListOpts::builder()
+            .input_dir(input_dir)
+            .output_dir(output_dir)
+            .fmeth(fmeth)
+            .expected_ori(expected_ori)
+            .version(VERSION)
+            .velo_mode(velo_mode)
+            .cmdline(&cmdline)
+            .log(&log)
+            .build();
+
+        match generate_permit_list(gpl_opts) {
             Ok(nc) if nc == 0 => {
                 warn!(log, "found 0 corrected barcodes; please check the input.");
             }
@@ -589,16 +591,11 @@ fn main() -> anyhow::Result<()> {
         let eq_label_file = t.value_of_t("eq-labels").unwrap();
         let filter_list = t.value_of("quant-subset");
         let usa_mode = t.is_present("usa");
-        //let bc_file = t.value_of_t("barcodes").unwrap();
 
         alevin_fry::infer::infer(
-            //num_bootstraps,
-            //init_uniform,
-            //summary_stat,
             count_mat,
             eq_label_file,
             usa_mode,
-            //bc_file,
             use_mtx,
             num_threads,
             filter_list,

src/prog_opts.rs

@@ -1,7 +1,11 @@
-use crate::quant::{ResolutionStrategy, SplicedAmbiguityModel};
 //use derive_builder::Builder;
+use bio_types::strand::Strand;
+use slog;
 use typed_builder::TypedBuilder;
 
+use crate::cellfilter::CellFilterMethod;
+use crate::quant::{ResolutionStrategy, SplicedAmbiguityModel};
+
 #[derive(TypedBuilder, Debug)]
 //#[builder(name = "QuantOptsBuilder")]
 pub struct QuantOpts<'a, 'b, 'c, 'd> {
@@ -24,3 +28,15 @@ pub struct QuantOpts<'a, 'b, 'c, 'd> {
     pub version: &'c str,
     pub log: &'d slog::Logger,
 }
+
+#[derive(TypedBuilder, Debug)]
+pub struct GenPermitListOpts<'a, 'b, 'c> {
+    pub input_dir: String,
+    pub output_dir: String,
+    pub fmeth: CellFilterMethod,
+    pub expected_ori: Strand,
+    pub velo_mode: bool,
+    pub cmdline: &'a str,
+    pub version: &'b str,
+    pub log: &'c slog::Logger,
+}