Thread --dict flag through simpleaf index to piscem

Adds `--dict {auto,sshash,tiny}` (default auto) to `simpleaf index`,
forwarded to the piscem build subprocess. Enables Tiny dictionary
artifacts for small references (transcriptomes, probe sets).

Author: rob-p

src/simpleaf_commands.rs

@@ -26,9 +26,27 @@ pub use self::workflow::{
 pub use crate::atac::commands::AtacCommand;
 pub use crate::defaults::{DefaultMappingParams, DefaultParams};
 
-use clap::{ArgGroup, Args, Subcommand, builder::ArgPredicate};
+use clap::{ArgGroup, Args, Subcommand, ValueEnum, builder::ArgPredicate};
 use std::path::PathBuf;
 
+/// Dictionary backend to request from piscem build / map commands.
+#[derive(ValueEnum, Clone, Copy, Debug, PartialEq, Eq)]
+pub enum PiscemDict {
+    Auto,
+    Sshash,
+    Tiny,
+}
+
+impl PiscemDict {
+    pub fn as_cli(&self) -> &'static str {
+        match self {
+            PiscemDict::Auto => "auto",
+            PiscemDict::Sshash => "sshash",
+            PiscemDict::Tiny => "tiny",
+        }
+    }
+}
+
 /// The type of references we might create
 /// to map against for quantification with
 /// alevin-fry.
@@ -356,6 +374,17 @@ pub struct IndexOpts {
     #[arg(long, display_order = 6)]
     pub overwrite: bool,
 
+    /// Piscem dictionary backend: `auto` (default, emits Tiny artifacts for
+    /// small references), `sshash` (compact), or `tiny` (fast-path).
+    #[arg(
+        long,
+        value_enum,
+        default_value_t = PiscemDict::Auto,
+        help_heading = "Piscem Index Options",
+        display_order = 7
+    )]
+    pub dict: PiscemDict,
+
     /// Number of threads to use when running
     #[arg(short, long, default_value_t = 16, display_order = 2)]
     pub threads: u32,

src/simpleaf_commands/indexing.rs

@@ -591,7 +591,9 @@ pub fn build_ref_and_index(af_home_path: &Path, opts: IndexOpts) -> anyhow::Resu
 
     piscem_index_cmd
         .arg("--threads")
-        .arg(format!("{}", threads));
+        .arg(format!("{}", threads))
+        .arg("--dict")
+        .arg(opts.dict.as_cli());
 
     if let Some(decoy_paths) = opts.decoy_paths {
         match prog_utils::check_version_constraints(