refactor(multiplex-quant): use forward/reverse for --sample-bc-ori

Per design discussion: keep the CLI vocabulary consistent with the
chemistry preset JSON (`sample_bc_ori: "forward" | "reverse"`) and with
alevin-fry's own `--sample-bc-ori` flag (also `forward` / `reverse`).
Drop the `fw`/`rev` shorthand and the in-process translation layer.

Author: an-altosian

src/simpleaf_commands.rs

@@ -573,13 +573,14 @@ pub struct MultiplexQuantOpts {
     #[arg(long, default_value = "both")]
     pub expected_ori: String,
 
-    /// Sample barcode orientation: `fw` (whitelist matches read as-is) or `rev`
-    /// (reverse-complement the whitelist before lookup). Overrides the chemistry
-    /// preset's `sample_bc_ori` when set. Useful for cycle-plan variants (e.g.
-    /// 10x Flex Configuration B) where the sample BC is read off the opposite
-    /// strand from the canonical preset. Shorthand mirrors `--expected-ori`.
+    /// Sample barcode orientation: `forward` (whitelist matches read as-is) or
+    /// `reverse` (reverse-complement the whitelist before lookup). Overrides
+    /// the chemistry preset's `sample_bc_ori` when set. Useful for cycle-plan
+    /// variants (e.g. 10x Flex Configuration B) where the sample BC is read
+    /// off the opposite strand from the canonical preset. Vocabulary matches
+    /// the preset JSON and alevin-fry's `--sample-bc-ori`.
     #[arg(long,
-        value_parser = clap::builder::PossibleValuesParser::new(["fw", "rev"]))]
+        value_parser = clap::builder::PossibleValuesParser::new(["forward", "reverse"]))]
     pub sample_bc_ori: Option<String>,
 
     /// Sample barcode correction mode

src/simpleaf_commands/multiplex_quant.rs

@@ -404,21 +404,16 @@ pub fn multiplex_map_and_quant(af_home: &Path, opts: MultiplexQuantOpts) -> anyh
         .arg(format!("{}", opts.min_reads));
 
     // Forward the sample-barcode orientation to alevin-fry. Precedence:
-    //   1. user-supplied --sample-bc-ori CLI override (`fw`/`rev` shorthand,
-    //      mirroring --expected-ori; translated to alevin-fry's
-    //      `forward`/`reverse` vocabulary below).
-    //   2. the chemistry preset's declared sample_bc_ori string (passed as-is;
-    //      already `forward` / `reverse` in the JSON).
+    //   1. user-supplied --sample-bc-ori CLI override (`forward` / `reverse`,
+    //      matching alevin-fry's vocabulary and the preset JSON).
+    //   2. the chemistry preset's declared sample_bc_ori (e.g. 10x Flex v2
+    //      where the whitelist is the RC of what appears on the read).
     //   3. omit the flag (alevin-fry default).
-    let sbc_ori_override = match opts.sample_bc_ori.as_deref() {
-        Some("fw") => Some("forward"),
-        Some("rev") => Some("reverse"),
-        Some(_) => unreachable!("clap PossibleValuesParser restricts to fw/rev"),
-        None => chem
-            .as_ref()
+    let sbc_ori_override = opts.sample_bc_ori.as_deref().or_else(|| {
+        chem.as_ref()
             .and_then(|c| c.sample_bc_list.as_ref())
-            .and_then(|s| s.sample_bc_ori.as_deref()),
-    };
+            .and_then(|s| s.sample_bc_ori.as_deref())
+    });
     if let Some(ori) = sbc_ori_override {
         gpl_cmd.arg("--sample-bc-ori").arg(ori);
     }