fix: update subtract tests to follow inheritance rules of scores. rem…

…ove score types from generic
noamteyssier · Feb 9, 2024 · 39a036f · 39a036f
1 parent aa2bf03
commit 39a036f
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Showing 9 changed files with 89 additions and 47 deletions.
diff --git a/src/commands/flank.rs b/src/commands/flank.rs
@@ -135,7 +135,7 @@ mod testing {
 
     #[test]
     fn test_flank_left_bed6() {
-        let iv = Bed6::new(1, 100, 400, 1, 2, Strand::default());
+        let iv = Bed6::new(1, 100, 400, 1, 2.into(), Strand::default());
         let left = left_flank(iv, 50).unwrap();
         assert_eq!(left.start(), 50);
         assert_eq!(left.end(), 100);
@@ -146,7 +146,20 @@ mod testing {
 
     #[test]
     fn test_flank_left_bed12() {
-        let iv = Bed12::new(1, 100, 400, 1, 2, Strand::default(), 3, 4, 5, 6, 7, 8);
+        let iv = Bed12::new(
+            1,
+            100,
+            400,
+            1,
+            2.into(),
+            Strand::default(),
+            3,
+            4,
+            5,
+            6,
+            7,
+            8,
+        );
         let left = left_flank(iv, 50).unwrap();
         assert_eq!(left.start(), 50);
         assert_eq!(left.end(), 100);
@@ -187,7 +200,7 @@ mod testing {
 
     #[test]
     fn test_flank_right_bed6() {
-        let iv = Bed6::new(1, 100, 400, 1, 2, Strand::default());
+        let iv = Bed6::new(1, 100, 400, 1, 2.into(), Strand::default());
         let right = right_flank(iv, 50, None).unwrap();
         assert_eq!(right.start(), 400);
         assert_eq!(right.end(), 450);
@@ -198,7 +211,20 @@ mod testing {
 
     #[test]
     fn test_flank_right_bed12() {
-        let iv = Bed12::new(1, 100, 400, 1, 2, Strand::default(), 3, 4, 5, 6, 7, 8);
+        let iv = Bed12::new(
+            1,
+            100,
+            400,
+            1,
+            2.into(),
+            Strand::default(),
+            3,
+            4,
+            5,
+            6,
+            7,
+            8,
+        );
         let right = right_flank(iv, 50, None).unwrap();
         assert_eq!(right.start(), 400);
         assert_eq!(right.end(), 450);

diff --git a/src/commands/random.rs b/src/commands/random.rs
@@ -4,7 +4,7 @@ use crate::{
     types::{Genome, InputFormat, NumericBed12, NumericBed3, NumericBed4, NumericBed6, Translater},
 };
 use anyhow::Result;
-use bedrs::Strand;
+use bedrs::{Score, Strand};
 use rand::Rng;
 use std::io::Write;
 
@@ -123,7 +123,7 @@ pub fn random_bed6<W: Write>(args: RandomArgs, writer: W) -> Result<()> {
             (c, x, y, s)
         })
         // build the interval
-        .map(|(c, x, y, s)| NumericBed6::new(c, x, y, 0, 0.0, s));
+        .map(|(c, x, y, s)| NumericBed6::new(c, x, y, 0, Score::Empty, s));
 
     write_records_iter_with(interval_gen, writer, genome_sizes.translater())?;
 
@@ -175,7 +175,7 @@ pub fn random_bed12<W: Write>(args: RandomArgs, writer: W) -> Result<()> {
             (c, x, y, t, u, s)
         })
         // build the interval
-        .map(|(c, x, y, t, u, s)| NumericBed12::new(c, x, y, 0, 0.0, s, t, u, 0, 0, 0, 0));
+        .map(|(c, x, y, t, u, s)| NumericBed12::new(c, x, y, 0, Score::Empty, s, t, u, 0, 0, 0, 0));
 
     write_records_iter_with(interval_gen, writer, genome_sizes.translater())?;
 

diff --git a/src/commands/shift.rs b/src/commands/shift.rs
@@ -162,7 +162,7 @@ mod testing {
 
     #[test]
     fn test_shift_bed6() {
-        let iv = Bed6::new(1, 100, 200, 1, 2, Strand::default());
+        let iv = Bed6::new(1, 100, 200, 1, 2.into(), Strand::default());
         let si = shift_interval(iv, 50.0, false, None);
         assert_eq!(si.start(), 150);
         assert_eq!(si.end(), 250);
@@ -173,7 +173,20 @@ mod testing {
 
     #[test]
     fn test_shift_bed12() {
-        let iv = Bed12::new(1, 100, 400, 1, 2, Strand::default(), 3, 4, 5, 6, 7, 8);
+        let iv = Bed12::new(
+            1,
+            100,
+            400,
+            1,
+            2.into(),
+            Strand::default(),
+            3,
+            4,
+            5,
+            6,
+            7,
+            8,
+        );
         let si = shift_interval(iv, 50.0, false, None);
         assert_eq!(si.start(), 150);
         assert_eq!(si.end(), 450);

diff --git a/src/io/iter.rs b/src/io/iter.rs
@@ -77,7 +77,7 @@ impl<'a, 'b, R: Read> Iterator for NamedIter<'a, 'b, R, NumericBed6> {
             record.start(),
             record.end(),
             *name_idx,
-            *record.score(),
+            record.score(),
             record.strand().unwrap_or_default(),
         );
         Some(iv)

diff --git a/src/io/read/bed12.rs b/src/io/read/bed12.rs
@@ -90,7 +90,7 @@ fn convert_bed12_set<R: Read>(reader: R, translater: &mut SplitTranslater) -> Re
             record.start(),
             record.end(),
             name_int,
-            *record.score(),
+            record.score(),
             record.strand().unwrap_or_default(),
             record.thick_start(),
             record.thick_end(),

diff --git a/src/io/read/bed6.rs b/src/io/read/bed6.rs
@@ -77,7 +77,7 @@ fn convert_bed6_set<R: Read>(reader: R, translater: &mut SplitTranslater) -> Res
             record.start(),
             record.end(),
             name_int,
-            *record.score(),
+            record.score(),
             record.strand().unwrap_or_default(),
         );
         set.insert(interval);

diff --git a/src/types/mod.rs b/src/types/mod.rs
@@ -19,13 +19,12 @@ pub type NumericBed4 = Bed4<usize, usize, usize>;
 pub type NamedBed4<'a> = Bed4<&'a str, usize, &'a str>;
 pub type Bed4Set = IntervalContainer<NumericBed4, usize, usize>;
 
-pub type NumericBed6 = Bed6<usize, usize, usize, f64>;
-pub type NamedBed6<'a> = Bed6<&'a str, usize, &'a str, f64>;
+pub type NumericBed6 = Bed6<usize, usize, usize>;
+pub type NamedBed6<'a> = Bed6<&'a str, usize, &'a str>;
 pub type Bed6Set = IntervalContainer<NumericBed6, usize, usize>;
 
-pub type NumericBed12 = Bed12<usize, usize, usize, f64, usize, usize, usize, usize, usize>;
-pub type NamedBed12<'a> =
-    Bed12<&'a str, usize, &'a str, f64, usize, usize, &'a str, &'a str, &'a str>;
+pub type NumericBed12 = Bed12<usize, usize, usize, usize, usize, usize, usize, usize>;
+pub type NamedBed12<'a> = Bed12<&'a str, usize, &'a str, usize, usize, &'a str, &'a str, &'a str>;
 pub type Bed12Set = IntervalContainer<NumericBed12, usize, usize>;
 
 pub type NumericMetaInterval = MetaInterval<usize, usize, usize>;

diff --git a/src/types/translate/rename.rs b/src/types/translate/rename.rs
@@ -35,7 +35,7 @@ impl<'a> Rename<'a, NumericBed6, NamedBed6<'a>> for Renamer {
             iv.start(),
             iv.end(),
             name,
-            *iv.score(),
+            iv.score(),
             iv.strand().unwrap_or_default(),
         )
     }
@@ -52,7 +52,7 @@ impl<'a> Rename<'a, NumericBed12, NamedBed12<'a>> for Renamer {
             iv.start(),
             iv.end(),
             name,
-            *iv.score(),
+            iv.score(),
             iv.strand().unwrap_or_default(),
             iv.thick_start(),
             iv.thick_end(),

diff --git a/tests/subtract.rs b/tests/subtract.rs
@@ -23,7 +23,7 @@ mod testing {
             .iter()
             .map(|(chr, start, end, name, score, strand)| {
                 format!(
-                    "{}\t{}\t{}\t{}\t{:.1}\t{}\n",
+                    "{}\t{}\t{}\t{}\t{:.3}\t{}\n",
                     chr, start, end, name, score, strand
                 )
             })
@@ -52,7 +52,7 @@ mod testing {
                     block_starts,
                 )| {
                     format!(
-                        "{}\t{}\t{}\t{}\t{:.1}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n",
+                        "{}\t{}\t{}\t{}\t{:.3}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n",
                         chr,
                         start,
                         end,
@@ -114,12 +114,12 @@ mod testing {
             .output()?;
 
         let expected = vec![
-            (1, 100, 120, 0, 0.0, '+'),
-            (1, 125, 150, 0, 0.0, '+'),
-            (1, 160, 300, 0, 0.0, '+'),
-            (1, 400, 460, 0, 0.0, '+'),
-            (1, 470, 475, 0, 0.0, '+'),
-            (1, 500, 550, 0, 0.0, '+'),
+            (1, 100, 120, 0, '.', '+'),
+            (1, 125, 150, 0, '.', '+'),
+            (1, 160, 300, 0, '.', '+'),
+            (1, 400, 460, 0, '.', '+'),
+            (1, 470, 475, 0, '.', '+'),
+            (1, 500, 550, 0, '.', '+'),
         ];
         let expected_str = build_expected_str_bed6(&expected);
         assert_eq!(output.stdout, expected_str.as_bytes());
@@ -141,12 +141,12 @@ mod testing {
             .output()?;
 
         let expected = vec![
-            (1, 100, 120, 0, 0.0, '+', 0, 0, 0, 0, 0, 0),
-            (1, 125, 150, 0, 0.0, '+', 0, 0, 0, 0, 0, 0),
-            (1, 160, 300, 0, 0.0, '+', 0, 0, 0, 0, 0, 0),
-            (1, 400, 460, 0, 0.0, '+', 0, 0, 0, 0, 0, 0),
-            (1, 470, 475, 0, 0.0, '+', 0, 0, 0, 0, 0, 0),
-            (1, 500, 550, 0, 0.0, '+', 0, 0, 0, 0, 0, 0),
+            (1, 100, 120, 0, ".", '+', 0, 0, 0, 0, 0, 0),
+            (1, 125, 150, 0, ".", '+', 0, 0, 0, 0, 0, 0),
+            (1, 160, 300, 0, ".", '+', 0, 0, 0, 0, 0, 0),
+            (1, 400, 460, 0, ".", '+', 0, 0, 0, 0, 0, 0),
+            (1, 470, 475, 0, ".", '+', 0, 0, 0, 0, 0, 0),
+            (1, 500, 550, 0, ".", '+', 0, 0, 0, 0, 0, 0),
         ];
         let expected_str = build_expected_str_bed12(&expected);
         assert_eq!(output.stdout, expected_str.as_bytes());
@@ -198,13 +198,13 @@ mod testing {
             .output()?;
 
         let expected = vec![
-            (1, 100, 120, 0, 0.0, '+'),
-            (1, 125, 150, 0, 0.0, '+'),
-            (1, 160, 200, 0, 0.0, '+'),
-            (1, 200, 300, 0, 0.0, '+'),
-            (1, 400, 460, 0, 0.0, '+'),
-            (1, 470, 475, 0, 0.0, '+'),
-            (1, 500, 550, 0, 0.0, '+'),
+            (1, 100, 120, 0, ".", '+'),
+            (1, 125, 150, 0, ".", '+'),
+            (1, 160, 200, 0, ".", '+'),
+            (1, 200, 300, 0, "0.0", '+'),
+            (1, 400, 460, 0, ".", '+'),
+            (1, 470, 475, 0, ".", '+'),
+            (1, 500, 550, 0, "0.0", '+'),
         ];
         let expected_str = build_expected_str_bed6(&expected);
         assert_eq!(output.stdout, expected_str.as_bytes());
@@ -227,15 +227,19 @@ mod testing {
             .output()?;
 
         let expected = vec![
-            (1, 100, 120, 0, 0.0, '+', 0, 0, 0, 0, 0, 0),
-            (1, 125, 150, 0, 0.0, '+', 0, 0, 0, 0, 0, 0),
-            (1, 160, 200, 0, 0.0, '+', 0, 0, 0, 0, 0, 0),
-            (1, 200, 300, 0, 0.0, '+', 0, 0, 0, 0, 0, 0),
-            (1, 400, 460, 0, 0.0, '+', 0, 0, 0, 0, 0, 0),
-            (1, 470, 475, 0, 0.0, '+', 0, 0, 0, 0, 0, 0),
-            (1, 500, 550, 0, 0.0, '+', 0, 0, 0, 0, 0, 0),
+            (1, 100, 120, 0, ".", '+', 0, 0, 0, 0, 0, 0),
+            (1, 125, 150, 0, ".", '+', 0, 0, 0, 0, 0, 0),
+            (1, 160, 200, 0, ".", '+', 0, 0, 0, 0, 0, 0),
+            (1, 200, 300, 0, "0.0", '+', 0, 0, 0, 0, 0, 0),
+            (1, 400, 460, 0, ".", '+', 0, 0, 0, 0, 0, 0),
+            (1, 470, 475, 0, ".", '+', 0, 0, 0, 0, 0, 0),
+            (1, 500, 550, 0, "0.0", '+', 0, 0, 0, 0, 0, 0),
         ];
         let expected_str = build_expected_str_bed12(&expected);
+
+        println!("{}", std::str::from_utf8(&output.stdout).unwrap());
+        println!("{}", expected_str);
+
         assert_eq!(output.stdout, expected_str.as_bytes());
         Ok(())
     }