feat: added ability to set expected-ori in quant

This commit adds the ability to set the `--expected-ori` option
that is passed to the `generate-permit-list` command of `alevin-fry`.

This is an "optional" option.  If it is not provided explicitly, it
is set to "both" (allowing reads aligning in both orientations to pass
through), unless the chemistry is set as 10xv2 or 10xv3, in which
case it is set as "fw".  Regardless of the chemistry, if the user sets
this option explicitly, their choice is respected.

Cargo.toml

@@ -33,7 +33,7 @@ categories = ["command-line-utilities", "science"]
 
 [dependencies]
 anyhow = "^1.0"
-clap = { version = ">=3.2.15", features = ["derive", "wrap_help", "cargo", "deprecated", "wrap_help"]} 
+clap = { version = ">=3.2.17", features = ["derive", "wrap_help", "cargo", "deprecated", "wrap_help"]} 
 cmd_lib = "^1.3.0"
 env_logger = "^0.9.0"
 log = "^0.4.17"

src/main.rs

@@ -159,6 +159,11 @@ enum Commands {
         #[clap(short = 's', long, help_heading = "mapping options", action)]
         use_selective_alignment: bool,
 
+        /// The expected direction/orientation of alignments in the chemistry being processed. If
+        /// not provided, will default to `fw` for 10xv2/10xv3, otherwise `both`.
+        #[clap(short = 'd', long, help_heading="permit list generation options", value_parser = clap::builder::PossibleValuesParser::new(["fw", "rc", "both"]))]
+        expected_ori: Option<String>,
+
         /// use knee filtering mode
         #[clap(short, long, help_heading = "permit list generation options", action)]
         knee: bool,
@@ -584,6 +589,7 @@ fn main() -> anyhow::Result<()> {
             reads2,
             mut threads,
             use_selective_alignment,
+            expected_ori,
             knee,
             unfiltered_pl,
             explicit_pl,
@@ -646,6 +652,25 @@ fn main() -> anyhow::Result<()> {
                 }
             };
 
+            let ori;
+            // if the user set the orientation, then
+            // use that explicitly
+            if let Some(o) = expected_ori {
+                ori = o;
+            } else {
+                // otherwise, this was not set explicitly. In that case
+                // if we have 10xv2 or 10xv3 chemistry, set ori = "fw"
+                // otherwise set ori = "both"
+                match chem {
+                    Chemistry::TenxV2 | Chemistry::TenxV3 => {
+                        ori = "fw".to_string();
+                    }
+                    _ => {
+                        ori = "both".to_string();
+                    }
+                }
+            }
+
             let mut filter_meth_opt = None;
 
             // based on the filtering method
@@ -796,7 +821,7 @@ fn main() -> anyhow::Result<()> {
 
             alevin_gpl_cmd.arg("generate-permit-list");
             alevin_gpl_cmd.arg("-i").arg(&map_output);
-            alevin_gpl_cmd.arg("-d").arg("fw");
+            alevin_gpl_cmd.arg("-d").arg(&ori);
 
             // add the filter mode
             add_to_args(&filter_meth, &mut alevin_gpl_cmd);