Minor clarity changes to variable names, etc.

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "recmap"
-version = "0.3.4"
+version = "0.3.5"
 edition = "2021"
 license = "MIT"
 authors = ["Vince Buffalo <[email protected]>"]

src/numeric.rs

@@ -82,7 +82,7 @@ pub fn recomb_dist_matrix<T: Float>(
  positions_x: &[T],
  positions_y: &[T],
  haldane: bool,
- min_rec: Option<T>,
+ rec_floor: Option<T>,
 ) -> Array2<T> {
  let mut dist_matrix = Array2::<T>::zeros((positions_x.len(), positions_y.len()));
  for (i, &pos_x) in positions_x.iter().enumerate() {
@@ -93,7 +93,7 @@ pub fn recomb_dist_matrix<T: Float>(
  } else {
  haldane_inverse(dist)
  };
- if let Some(min_rec_rate) = min_rec {
+ if let Some(min_rec_rate) = rec_floor {
  rf = rf.max(min_rec_rate);
  }
  dist_matrix[[i, j]] = rf;
@@ -164,7 +164,7 @@ where
  let y2 = ToPrimitive::to_f64(&y[idx])?;
  let x0 = ToPrimitive::to_f64(&x0)?;
 
- // Perform linear interpolation
+ // linear interpolation
  let y0 = y1 + (y2 - y1) * (x0 - x1) / (x2 - x1);
 
  NumCast::from(y0)

src/recmap.rs

@@ -176,14 +176,13 @@ impl RateMap {
  self.rates
  .iter()
  .zip(self.span().iter())
- .map(|(&x, &y)| x * y as RateFloat)
+ .map(|(&rate, &span)| rate * span as RateFloat)
  .collect()
  }
 
- /// Calculate the cumulative map length at each position.
+ /// Calculate the cumulative map length in Morgans at each position.
  pub fn calc_cumulative_mass(&mut self) {
  let mass = self.mass();
- //println!("mass: {:?}", mass);
  let cumulative_sum: Vec<_> = mass
  .iter()
  .scan(0.0, |state, &x| {
@@ -358,7 +357,8 @@ impl RecMap {
  new_rate_map.ends.push(end);
  new_rate_map.rates.push(rate);
 
- // if there is a fourth column, let's use it for validation
+ // if there is a fourth column, we could use it for validation
+ // TODO
  if has_fourth_column {
  //new_rate_map.calc_cumulative_mass();
  //assert_floats_eq(&new_rate_map.map_pos, map_positions.as_slice(), 0.01);
@@ -392,6 +392,8 @@ impl RecMap {
  map: rec_map,
  metadata,
  };
+ // generate the map positions from the marker positions
+ // and the per-basepair rates..
  rec_map.generate_map_positions();
  Ok(rec_map)
  }
@@ -434,7 +436,9 @@ impl RecMap {
  .get(name)
  .ok_or(RecMapError::NoChrom(name.to_string()))?;
  let ends = &rate_map.ends;
- let interp_result = interp1d(&ends[0..ends.len() - 1], &rate_map.map_pos, position);
+ let interp_result = interp1d(&ends[0..ends.len() - 1], 
+ &rate_map.map_pos, 
+ position);
  let interpolated_map_pos =
  interp_result.ok_or(RecMapError::LookupOutOfBounds(name.to_string(), position))?;
  Ok(interpolated_map_pos)
@@ -480,11 +484,11 @@ impl RecMap {
  positions_x: &[Position],
  positions_y: &[Position],
  haldane: bool,
- min_rec: Option<RateFloat>,
+ rec_floor: Option<RateFloat>,
  ) -> Result<Array2<RateFloat>, RecMapError> {
  let x_pos = self.interpolate_map_positions(chrom, positions_x)?;
  let y_pos = self.interpolate_map_positions(chrom, positions_y)?;
- Ok(recomb_dist_matrix(&x_pos, &y_pos, haldane, min_rec))
+ Ok(recomb_dist_matrix(&x_pos, &y_pos, haldane, rec_floor))
  }
 
  /// Write recombination map to HapMap-formatted file.
@@ -665,7 +669,7 @@ mod tests {
  &chr1_map.map_pos,
  &to_morgans(vec![0.0, 5.5, 13., 34.65]),
  1e-3,
- );
+  );
  }
 
  #[test]