add lib64 to path even without conda build, bump deps

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "piscem"
-version = "0.10.0"
+version = "0.10.1"
 edition = "2021"
 build = "build.rs"
 repository = "https://github.com/COMBINE-lab/piscem"
@@ -13,7 +13,7 @@ cmake = "0.1.50"
 [dependencies]
 num_cpus = "1.16.0"
 anyhow = "1.0.86"
-clap = { version = "4.5.8", features = ["cargo", "derive", "env", "wrap_help"] }
+clap = { version = "4.5.9", features = ["cargo", "derive", "env", "wrap_help"] }
 tracing = "0.1.40"
 tracing-subscriber = { version = "0.3.18", default-features = true, features = ["env-filter"] }
 prepare_fasta = "0.1.0"

build.rs

@@ -8,7 +8,14 @@ fn main() {
     let nopie_build = env::var("NOPIE");
     let nobmi2_var = env::var("NO_BMI2");
 
-    let mut is_conda_build = false;
+    let is_conda_build = match conda_build {
+        Ok(val) => match val.to_uppercase().as_str() {
+            "TRUE" | "1" | "YES" => true,
+            "FALSE" | "0" | "NO" => false,
+            _ => true,
+        },
+        Err(_e) => false,
+    };
 
     println!("cargo:rerun-if-changed=cuttlefish/CMakeLists.txt");
     println!("cargo:rerun-if-changed=piscem-cpp/CMakeLists.txt");
@@ -27,11 +34,10 @@ fn main() {
         (*cfg_cf).define("CMAKE_CXX_COMPILER", cxx_var);
     }
 
-    if let Ok(_conda_build) = conda_build {
+    if is_conda_build {
         (*cfg_cf).define("CONDA_BUILD", "TRUE");
         (*cfg_cf).define("CMAKE_OSX_DEPLOYMENT_TARGET", "10.15");
         (*cfg_cf).define("MACOSX_SDK_VERSION", "10.15");
-        is_conda_build = true;
     }
 
     if let Ok(nobmi2) = nobmi2_var {
@@ -67,21 +73,19 @@ fn main() {
         dst_piscem_cpp.join("lib").display()
     );
 
-    if is_conda_build {
-        // For some reason, if we are using
-        // conda and we are building for the
-        // linux target; things get put in the
-        // lib64 directory rather than lib...
-        // So, we add that here
-        println!(
-            "cargo:rustc-link-search=native={}",
-            dst_cf.join("lib64").display()
-        );
-        println!(
-            "cargo:rustc-link-search=native={}",
-            dst_piscem_cpp.join("lib64").display()
-        );
-    }
+    // For some reason, if we are using
+    // *some* linux distros (and on conda) and are
+    // building for the linux target;
+    // things get put in the lib64 directory
+    // rather than lib... So, we add that here
+    println!(
+        "cargo:rustc-link-search=native={}",
+        dst_cf.join("lib64").display()
+    );
+    println!(
+        "cargo:rustc-link-search=native={}",
+        dst_piscem_cpp.join("lib64").display()
+    );
 
     println!("cargo:rustc-link-lib=static=kmc_core");
     //println!("cargo:rustc-link-lib=static=pesc_static");

src/piscem_commands.rs

@@ -124,6 +124,10 @@ pub(crate) struct MapSCOpts {
     #[arg(short, long, help_heading = "Input")]
     pub index: String,
 
+    /// list available geometries supported by the underlying `pesc-sc` mapper
+    // #[arg(long, help_heading = "Advanced")]
+    // pub list_geometries: bool,
+
     /// geometry of barcode, umi and read
     #[arg(short, long)]
     pub geometry: String,
@@ -332,6 +336,10 @@ impl AsArgv for MapSCOpts {
             CString::new(self.output.as_str()).unwrap(),
         ];
 
+        /*if self.list_geometries {
+            args.push(CString::new("--list-geometries").unwrap());
+        }*/
+
         if self.ignore_ambig_hits {
             args.push(CString::new("--ignore-ambig-hits").unwrap());
         } else {