working and clippy

quinlan-lab · Dec 14, 2023 · 2cc5015 · 2cc5015
1 parent 5c1806a
commit 2cc5015
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Showing 4 changed files with 69 additions and 9 deletions.
diff --git a/benches/random_intervals.rs b/benches/random_intervals.rs
@@ -21,19 +21,19 @@ impl Intervals {
     fn new(name: String, n_intervals: usize, interval_len: u64) -> Self {
         Intervals {
             i: 0,
-            name: name,
+            name,
             n_intervals,
             curr_max: 1.0,
             rng: rand::thread_rng(),
-            interval_len: interval_len,
+            interval_len,
             saved_chrom: String::from("chr1"),
         }
     }
 }
 
 impl PositionedIterator for Intervals {
     fn name(&self) -> String {
-        String::from(format!("{}:{}", self.name, self.i))
+        format!("{}:{}", self.name, self.i)
     }
 
     fn next_position(&mut self, _q: Option<&Position>) -> Option<io::Result<Position>> {
@@ -44,7 +44,7 @@ impl PositionedIterator for Intervals {
             let start = ((1.0 - self.curr_max) * (MAX_POSITION as f64)) as u64;
             Some(Ok(Position::Interval(Interval {
                 chrom: self.saved_chrom.clone(),
-                start: start,
+                start,
                 stop: start + self.interval_len,
                 ..Default::default()
             })))

diff --git a/src/intersection.rs b/src/intersection.rs
@@ -387,7 +387,7 @@ mod tests {
                 name,
                 ivs: ivs
                     .into_iter()
-                    .map(|i| Position::Interval(i))
+                    .map(Position::Interval)
                     .collect::<Vec<Position>>(),
             }
         }
@@ -450,7 +450,7 @@ mod tests {
             }
         }
 
-        b_ivs.ivs.sort_by(|a, b| a.start().cmp(&b.start()));
+        b_ivs.ivs.sort_by_key(|a| a.start());
 
         let a_ivs: Box<dyn PositionedIterator> = Box::new(a_ivs);
 

diff --git a/src/intersections.rs b/src/intersections.rs
@@ -3,7 +3,6 @@ use crate::position::Position;
 #[allow(unused_imports)]
 use crate::string::String;
 use bitflags::bitflags;
-use std::ops::Deref;
 use std::sync::Arc;
 
 bitflags! {
@@ -294,6 +293,67 @@ mod tests {
         assert_eq!(rf.b[1].start(), 8);
         assert_eq!(rf.b[1].stop(), 12);
     }
+    // TODO: test Not
+
+    #[test]
+    fn test_a_pieces() {
+        let intersections = make_example("a: 1-10\nb: 3-6, 8-12");
+        let r = intersections.report(
+            IntersectionMode::PerPiece,
+            IntersectionMode::Default,
+            IntersectionPart::Whole,
+            IntersectionPart::Whole,
+            OverlapAmount::Bases(1),
+            OverlapAmount::Bases(1),
+        );
+        assert_eq!(r.len(), 2);
+        let rf = &r[0];
+        // test that a is 1-10
+        assert_eq!(rf.a.as_ref().unwrap().start(), 1);
+        assert_eq!(rf.a.as_ref().unwrap().stop(), 10);
+        // test that b is 3-6
+        assert_eq!(rf.b.len(), 1);
+        assert_eq!(rf.b[0].start(), 3);
+        assert_eq!(rf.b[0].stop(), 6);
+
+        let rf = &r[1];
+        assert_eq!(rf.a.as_ref().unwrap().start(), 1);
+        assert_eq!(rf.a.as_ref().unwrap().stop(), 10);
+        assert_eq!(rf.b.len(), 1);
+        assert_eq!(rf.b[0].start(), 8);
+        assert_eq!(rf.b[0].stop(), 12);
+    }
+
+    #[test]
+    fn test_a_pieces_ab_part() {
+        let intersections = make_example("a: 1-10\nb: 3-6, 8-12");
+        let r = intersections.report(
+            IntersectionMode::PerPiece,
+            IntersectionMode::Default,
+            IntersectionPart::Part,
+            IntersectionPart::Part,
+            OverlapAmount::Bases(1),
+            OverlapAmount::Bases(1),
+        );
+        // a: 3-6, b: 3-6
+        // a: 8-10, b: 8-10
+        assert_eq!(r.len(), 2);
+        let rf = &r[0];
+        // test that a is 3-6
+        assert_eq!(rf.a.as_ref().unwrap().start(), 3);
+        assert_eq!(rf.a.as_ref().unwrap().stop(), 6);
+        // test that b is 3-6
+        assert_eq!(rf.b.len(), 1);
+        assert_eq!(rf.b[0].start(), 3);
+        assert_eq!(rf.b[0].stop(), 6);
+
+        let rf = &r[1];
+        assert_eq!(rf.a.as_ref().unwrap().start(), 8);
+        assert_eq!(rf.a.as_ref().unwrap().stop(), 10);
+        assert_eq!(rf.b.len(), 1);
+        assert_eq!(rf.b[0].start(), 8);
+        assert_eq!(rf.b[0].stop(), 10);
+    }
 
     #[test]
     fn test_b_part() {

diff --git a/src/sniff.rs b/src/sniff.rs
@@ -34,8 +34,8 @@ where
     P: AsRef<Path>,
 {
     let file = std::fs::File::open(&path)?;
-    let r = open_reader(file, path);
-    r
+
+    open_reader(file, path)
 }
 
 pub fn open_reader<R, P>(reader: R, path: P) -> std::io::Result<Box<dyn PositionedIterator>>