From 587b0cb11d112d32a59b931a4f774ccbf57b6f5c Mon Sep 17 00:00:00 2001
From: Vince Buffalo <vsbuffalo@gmail.com>
Date: Thu, 7 Mar 2024 13:56:48 -0800
Subject: [PATCH] New GRanges::coverage() method, and metadata support for TSV
 output.

---
 src/commands.rs | 10 ++++++++++
 src/granges.rs  | 23 ++++++++++++++++++++++-
 src/io/tsv.rs   |  2 ++
 3 files changed, 34 insertions(+), 1 deletion(-)

diff --git a/src/commands.rs b/src/commands.rs
index 771135e..45a1ef9 100644
--- a/src/commands.rs
+++ b/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)?;
         }
diff --git a/src/granges.rs b/src/granges.rs
index 9f386b1..43b487e 100644
--- a/src/granges.rs
+++ b/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>> {
diff --git a/src/io/tsv.rs b/src/io/tsv.rs
index 0f99fb7..c5f737a 100644
--- a/src/io/tsv.rs
+++ b/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>>
 }