New GRanges::coverage() method, and metadata support for TSV output.

src/commands.rs

@@ -57,6 +57,14 @@ pub fn build_tsv_writer_with_config(
  None => Box::new(io::stdout()),
  };
 
+ // Write metadata, if there.
+ if let Some(metadata_rows) = &config.metadata {
+ for metadata_row in metadata_rows {
+ writeln!(writer_boxed, "#{}", metadata_row)?;
+ }
+ }
+
+ // Write headers, if there.
  if let Some(headers) = &config.headers {
  writeln!(writer_boxed, "{}", headers.join("\t"))?;
  }
@@ -955,6 +963,7 @@ impl FeatureDensity {
  let config = TsvConfig {
  no_value_string: "NA".to_string(),
  headers: Some(headers),
+ metadata: None,
  };
  window_counts.write_to_tsv(self.output.as_ref(), &config)?;
  }
@@ -966,6 +975,7 @@ impl FeatureDensity {
  let config = TsvConfig {
  no_value_string: "NA".to_string(),
  headers: Some(headers),
+ metadata: None,
  };
  window_counts.write_to_tsv(self.output.as_ref(), &config)?;
  }

src/granges.rs

@@ -133,11 +133,14 @@ where
  std::mem::take(&mut self.ranges)
  }
 
+ /// Take both the ranges and data from a [`GRanges`] object,
+ /// returning them in a tuple.
  pub fn take_both(&mut self) -> Result<(GenomeMap<C>, T), GRangesError> {
  let data = std::mem::take(&mut self.data).ok_or(GRangesError::NoDataContainer)?;
  let ranges = std::mem::take(&mut self.ranges);
  Ok((ranges, data))
  }
+
 }
 
 impl<C, T> GRanges<C, T>
@@ -219,8 +222,9 @@ impl<'a, C, T> AsGRangesRef<'a, C, T> for GRanges<C, T> {
  }
 }
 
-impl<'a, T> GenomicRangesTsvSerialize<'a, VecRangesIndexed> for GRanges<VecRangesIndexed, T>
+impl<'a, C, T> GenomicRangesTsvSerialize<'a, C> for GRanges<C, T>
 where
+ C: IterableRangeContainer,
  T: IndexedDataContainer + 'a,
  <T as IndexedDataContainer>::Item<'a>: Serialize,
 {
@@ -439,6 +443,18 @@ where
  }
  Ok(all_midpoints)
  }
+
+ /// Get the total coverage (the sum of all range widths).
+ pub fn coverage(&self) -> Position {
+ let mut coverage = 0;
+ for (_seqname, ranges) in self.ranges.iter() {
+ for range in ranges.iter_ranges() {
+ coverage += range.width()
+ }
+ }
+ coverage
+ }
+
 }
 
 impl<C, T> GRanges<C, T>
@@ -702,6 +718,11 @@ where
  pub fn midpoints(&self) -> Result<GenomeMap<Vec<Position>>, GRangesError> {
  self.0.midpoints()
  }
+
+ /// Get the total coverage (the sum of all range widths).
+ pub fn coverage(&self) -> Position {
+ self.0.coverage()
+ }
 }
 
 impl<U> GRanges<VecRangesIndexed, Vec<U>> {

src/io/tsv.rs

@@ -7,6 +7,7 @@ lazy_static! {
  pub static ref BED_TSV: TsvConfig = TsvConfig {
  no_value_string: ".".to_string(),
  headers: None,
+ metadata: None,
  };
 }
 
@@ -17,4 +18,5 @@ lazy_static! {
 pub struct TsvConfig {
  pub no_value_string: String,
  pub headers: Option<Vec<String>>,
+ pub metadata: Option<Vec<String>>
 }