refactor: update file names to avoid nested mod conflicts

src/commands/intersect/mod.rs

@@ -1,3 +1,3 @@
-mod intersect;
 mod iter;
-pub use intersect::intersect;
+mod run;
+pub use run::intersect;

src/types/formats/formats.rs → src/types/formats/in_formats.rs

@@ -92,16 +92,16 @@ mod testing {
         let lines = "1\t1\t2\n1\t3\t4\n1\t5\t6\n".as_bytes();
         let mut reader = BufReader::new(lines);
         reader.fill_buf().unwrap();
-        let _input_format = InputFormat::predict(&mut reader).unwrap();
+        let _input_format = InputFormat::predict(&reader).unwrap();
         let num_lines = reader.lines().count();
         assert_eq!(num_lines, 3);
     }
 
     #[test]
     fn no_consumption_field_format() {
         let lines = "1\t1\t2\n1\t3\t4\n1\t5\t6\n".as_bytes();
-        let mut reader = BufReader::new(lines);
-        let _field_format = FieldFormat::predict(&mut reader, InputFormat::Bed3).unwrap();
+        let reader = BufReader::new(lines);
+        let _field_format = FieldFormat::predict(&reader, InputFormat::Bed3).unwrap();
         let num_lines = reader.lines().count();
         assert_eq!(num_lines, 3);
     }

src/types/formats/mod.rs

@@ -1,8 +1,8 @@
-mod formats;
 mod genome;
+mod in_formats;
 use bedrs::{Bed12, Bed3, Bed6, IntervalContainer};
-pub use formats::{FieldFormat, InputFormat};
 pub use genome::Genome;
+pub use in_formats::{FieldFormat, InputFormat};
 
 pub type NumericBed3 = Bed3<usize, usize>;
 pub type NamedBed3<'a> = Bed3<&'a str, usize>;