add missing file

src/cmd_parse_utils.rs

@@ -0,0 +1,71 @@
+use crate::quant::{ResolutionStrategy, SplicedAmbiguityModel};
+use clap;
+use std::path::{Path, PathBuf};
+
+impl clap::ValueEnum for ResolutionStrategy {
+    fn value_variants<'a>() -> &'a [Self] {
+        &[
+            Self::Trivial,
+            Self::CellRangerLike,
+            Self::CellRangerLikeEm,
+            Self::ParsimonyEm,
+            Self::Parsimony,
+            Self::ParsimonyGeneEm,
+            Self::ParsimonyGene,
+        ]
+    }
+
+    fn to_possible_value<'a>(&self) -> Option<clap::PossibleValue<'a>> {
+        match self {
+            Self::Trivial => Some(clap::PossibleValue::new("trivial")),
+            Self::CellRangerLike => Some(clap::PossibleValue::new("cr-like")),
+            Self::CellRangerLikeEm => Some(clap::PossibleValue::new("cr-like-em")),
+            Self::ParsimonyEm => Some(clap::PossibleValue::new("parsimony-em")),
+            Self::Parsimony => Some(clap::PossibleValue::new("parsimony")),
+            Self::ParsimonyGeneEm => Some(clap::PossibleValue::new("parsimony-gene-em")),
+            Self::ParsimonyGene => Some(clap::PossibleValue::new("parsimony-gene")),
+        }
+    }
+}
+
+impl clap::ValueEnum for SplicedAmbiguityModel {
+    fn value_variants<'a>() -> &'a [Self] {
+        &[Self::PreferAmbiguity, Self::WinnerTakeAll]
+    }
+
+    fn to_possible_value<'a>(&self) -> Option<clap::PossibleValue<'a>> {
+        match self {
+            Self::PreferAmbiguity => Some(clap::PossibleValue::new("prefer-ambig")),
+            Self::WinnerTakeAll => Some(clap::PossibleValue::new("winner-take-all")),
+        }
+    }
+}
+
+/// Checks if the path pointed to by v exists.  It can be
+/// any valid entity (e.g. disk file, FIFO, directory, etc.).
+/// If there is any issue with permissions or failure to properly
+/// resolve symlinks, or if the path is wrong, it returns
+/// an Err(String), else Ok(PathBuf).
+pub fn pathbuf_file_exists_validator(v: &str) -> Result<PathBuf, String> {
+    // NOTE: we explicitly *do not* check `is_file()` here
+    // since we want to return true even if the path is to
+    // a FIFO/named pipe.
+    if !Path::new(v).exists() {
+        Err(String::from("No valid file was found at this path."))
+    } else {
+        Ok(PathBuf::from(v))
+    }
+}
+
+/// Checks if the path pointed to by v exists and is
+/// a valid directory on disk.  If there is any issue
+/// with permissions or failure to properly
+/// resolve symlinks, or if the path is wrong, it returns
+/// an Err(String), else Ok(PathBuf).
+pub fn pathbuf_directory_exists_validator(v: &str) -> Result<PathBuf, String> {
+    if !Path::new(v).is_dir() {
+        Err(String::from("No valid directory was found at this path."))
+    } else {
+        Ok(PathBuf::from(v))
+    }
+}