clean up

src/collate.rs

@@ -43,7 +43,6 @@ pub fn collate(
     //expected_ori: Strand,
     log: &slog::Logger,
 ) -> anyhow::Result<()> {
-    //}, Box<dyn std::error::Error>> {
     let parent = std::path::Path::new(&input_dir);
 
     // open the metadata file and read the json
@@ -258,7 +257,6 @@ pub fn collate_with_temp(
     version: &str,
     log: &slog::Logger,
 ) -> anyhow::Result<()> {
-    //Box<dyn std::error::Error>> {
     // the number of corrected cells we'll write
     let expected_output_chunks = tsv_map.len() as u64;
     // the parent input directory

src/convert.rs

@@ -6,6 +6,8 @@
  *
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */
+
+use anyhow::Context;
 use indicatif::{ProgressBar, ProgressStyle};
 use slog::{crit, info};
 //use num_format::{Locale};
@@ -493,7 +495,7 @@ pub fn view2(
     print_header: bool,
     _out_file: String,
     log: &slog::Logger,
-) -> Result<u64, Box<dyn std::error::Error>> {
+) -> anyhow::Result<u64> { 
     let i_file = File::open(rad_file).unwrap();
     let mut br = BufReader::new(i_file);
     let hdr = rad_types::RadHeader::from_bytes(&mut br);
@@ -548,9 +550,9 @@ pub fn view2(
     let mut num_reads: u64 = 0;
 
     let bc_type = rad_types::decode_int_type_tag(bct.expect("no barcode tag description present."))
-        .expect("unknown barcode type id.");
+        .context("unknown barcode type id.")?;
     let umi_type = rad_types::decode_int_type_tag(umit.expect("no umi tag description present"))
-        .expect("unknown barcode type id.");
+        .context("unknown barcode type id.")?;
 
     let stdout = stdout(); // get the global stdout entity
     let stdout_l = stdout.lock();

src/infer.rs

@@ -40,7 +40,6 @@ pub fn infer(
     output_dir: String,
     log: &slog::Logger,
 ) -> anyhow::Result<()> {
-    // Box<dyn std::error::Error>> {
     info!(
         log,
         "inferring abundances from equivalence class count input."

src/main.rs

@@ -40,7 +40,6 @@ fn gen_random_kmer(k: usize) -> String {
 }
 
 fn main() -> anyhow::Result<()> {
-    //}, Box<dyn std::error::Error>> {
     let num_hardware_threads = num_cpus::get() as u32;
     let max_num_threads: String = (num_cpus::get() as u32).to_string();
     let max_num_collate_threads: String = (16_u32.min(num_hardware_threads).max(2_u32)).to_string();
@@ -186,25 +185,6 @@ fn main() -> anyhow::Result<()> {
 
     // You can handle information about subcommands by requesting their matches by name
     // (as below), requesting just the name used, or both at the same time
-    /*
-    if let Some(ref t) = opts.subcommand_matches("test") {
-        let input_file: String = t.value_of_t("input").expect("no input string specified");
-        let rad_dir: String = t.value_of_t("rad-dir").expect("no input string specified");
-        let min_reads: usize = t
-            .value_of_t("min-reads")
-            .expect("min-reads must be a valid integer");
-        if min_reads < 1 {
-            crit!(
-                log,
-                "min-reads < 1 is not supported, the value {} was provided",
-                min_reads
-            );
-            std::process::exit(1);
-        }
-        let _r = test_external_parse(input_file, rad_dir, min_reads, &log);
-    }
-    */
-
     if let Some(t) = opts.subcommand_matches("generate-permit-list") {
         let input_dir: String = t.value_of_t("input").expect("no input directory specified");
         let output_dir: String = t