tweak around

src/simpleaf_commands.rs

@@ -479,7 +479,7 @@ pub struct ChemistryAddOpts {
     /// the geometry to which the chemistry maps, wrapped in quotes.
     #[arg(short, long)]
     pub geometry: String,
-    /// the expected orientation indicating the direction to the reference sequences.
+    /// the expected orientation indicating the direction of biological reads to reference sequences.
     #[arg(short, long, value_parser = clap::builder::PossibleValuesParser::new(["fw", "rc", "both"]))]
     pub expected_ori: String,
     /// the (fully-qualified) path to a local file that will be copied into

src/simpleaf_commands/quant.rs

@@ -386,8 +386,8 @@ pub fn map_and_quant(af_home_path: &Path, opts: MapQuantOpts) -> anyhow::Result<
     let ori: ExpectedOri;
     // if the user set the orientation, then
     // use that explicitly
-    if let Some(o) = opts.expected_ori.clone() {
-        ori = ExpectedOri::from_str(&o).with_context(|| {
+    if let Some(o) = &opts.expected_ori {
+        ori = ExpectedOri::from_str(o).with_context(|| {
             format!(
                 "Could not parse orientation {}. It must be one of the following: {:?}",
                 o,

src/utils/af_utils.rs

@@ -14,7 +14,7 @@ use strum_macros::EnumIter;
 use tracing::{error, info, warn};
 
 use crate::atac::commands::AtacChemistry;
-use crate::utils::chem_utils::CustomChemistry;
+use crate::utils::chem_utils::{get_single_custom_chem_from_file, CustomChemistry};
 use crate::utils::{self, prog_utils};
 
 use super::chem_utils::{QueryInRegistry, LOCAL_PL_PATH_KEY, REMOTE_PL_URL_KEY};
@@ -201,6 +201,7 @@ impl Chemistry {
                 // and when we propagate more information about paired-end mappings.
                 ExpectedOri::Forward
             }
+            Chemistry::Rna(RnaChemistry::Other(_)) => ExpectedOri::default(),
             _ => ExpectedOri::default(),
         }
     }
@@ -225,7 +226,7 @@ impl Chemistry {
             s => {
                 // first, we check if the chemistry is a known chemistry for the given mapper
                 // Second, we check if its a registered custom chemistry
-                // Third, we check if its a custom chemistry string
+                // Third, we check if its a custom geometry string
                 if index_type.is_known_chem(s) {
                     Chemistry::Rna(RnaChemistry::Other(s.to_string()))
                 } else if let Some(chem) =

src/utils/chem_utils.rs

@@ -107,13 +107,8 @@ impl CustomChemistry {
     }
 
     /// Parse the value that corresponds to a key in the top-level custom chemistry JSON object.
-    /// The key ONLY is used for error messages and assigning the name field of the CustomChemistry struct.
+    /// The key is ONLY used for error messages and assigning the name field of the CustomChemistry struct.
     /// The value must be an json value object with a valid geometry field that can be parsed into a CustomChemistry struct.
-    /// The value corresponding to this key can be either
-    ///     1. An object having the associated / expected keys
-    ///     2. A string representing the geometry
-    /// The second case here is legacy from older versions of simpleaf and deprecated, so we should
-    /// warn by default when we see it.
     pub fn from_value(key: &str, value: &Value) -> Result<CustomChemistry> {
         match value {
             // deprecated case. Need to warn and return an error