use enum instead of dyn to next_interval

benches/random_intervals.rs

@@ -1,7 +1,7 @@
 use bedder::chrom_ordering::parse_genome;
 use bedder::intersection::IntersectionIterator;
 use bedder::interval::Interval;
-use bedder::position::{Position, Positioned, PositionedIterator};
+use bedder::position::{Position, PositionedIterator};
 use bedder::string::String;
 use criterion::{black_box, criterion_group, criterion_main, Criterion};
 use rand::Rng;
@@ -36,7 +36,7 @@ impl PositionedIterator for Intervals {
         String::from(format!("{}:{}", self.name, self.i))
     }
 
-    fn next_position(&mut self, _q: Option<&dyn Positioned>) -> Option<io::Result<Position>> {
+    fn next_position(&mut self, _q: Option<&Position>) -> Option<io::Result<Position>> {
         if self.i < self.n_intervals {
             self.i += 1;
             let r: f64 = self.rng.gen();

examples/intersect_bed_count.rs

@@ -7,7 +7,6 @@ use clap::Parser;
 extern crate bedder;
 use crate::bedder::chrom_ordering::parse_genome;
 use crate::bedder::intersection::IntersectionIterator;
-use crate::bedder::position::Positioned;
 
 #[derive(Parser, Debug)]
 struct Args {

src/bedder_bed.rs

@@ -71,7 +71,7 @@ where
 {
     fn next_position(
         &mut self,
-        _q: Option<&dyn crate::position::Positioned>,
+        _q: Option<&crate::position::Position>,
     ) -> Option<std::result::Result<Position, std::io::Error>> {
         self.buf.clear();
         loop {

src/bedder_vcf.rs

@@ -163,7 +163,7 @@ impl Positioned for vcf::record::Record {
 impl<'a> crate::position::PositionedIterator for BedderVCF<'a> {
     fn next_position(
         &mut self,
-        _q: Option<&dyn crate::position::Positioned>,
+        _q: Option<&crate::position::Position>,
     ) -> Option<std::result::Result<Position, std::io::Error>> {
         let mut v = vcf::Record::default();
 
@@ -177,7 +177,7 @@ impl<'a> crate::position::PositionedIterator for BedderVCF<'a> {
         }
     }
     fn name(&self) -> String {
-        String::from("vcf")
+        String::from("vcf line number:") + &self.record_number.to_string()
     }
 }
 

src/intersection.rs

@@ -8,7 +8,7 @@ use std::io::{Error, ErrorKind};
 use std::rc::Rc;
 //use std::sync::Arc as Rc;
 
-use crate::position::{Position, Positioned, PositionedIterator};
+use crate::position::{Position, PositionedIterator};
 
 /// An iterator that returns the intersection of multiple iterators.
 pub struct IntersectionIterator<'a> {
@@ -299,7 +299,7 @@ impl<'a> IntersectionIterator<'a> {
                 .expect("expected interval iterator at file index");
             // for a given base_interval, we make sure to call next_position with Some, only once.
             // subsequent calls will be with None.
-            let arg: Option<&dyn Positioned> = if !self.called[file_index] {
+            let arg: Option<&Position> = if !self.called[file_index] {
                 self.called[file_index] = true;
                 Some(base_interval.as_ref())
             } else {
@@ -392,7 +392,7 @@ mod tests {
             String::from(format!("{}:{}", self.name, self.i))
         }
 
-        fn next_position(&mut self, _o: Option<&dyn Positioned>) -> Option<io::Result<Position>> {
+        fn next_position(&mut self, _o: Option<&Position>) -> Option<io::Result<Position>> {
             if self.i >= self.ivs.len() {
                 return None;
             }

src/interval.rs

@@ -1,4 +1,4 @@
-use crate::position::{Field, FieldError, Positioned, Value};
+use crate::position::{Field, FieldError, Value};
 use crate::string::String;
 /// Interval type is a simple struct that can be used as a default interval type.
 /// It has a chromosome, start, and stop field along with a (linear) HashMap of Values.
@@ -13,22 +13,22 @@ pub struct Interval {
     pub fields: LinearMap<String, Value>,
 }
 
-impl Positioned for Interval {
+impl Interval {
     #[inline]
-    fn start(&self) -> u64 {
+    pub fn start(&self) -> u64 {
         self.start
     }
     #[inline]
-    fn stop(&self) -> u64 {
+    pub fn stop(&self) -> u64 {
         self.stop
     }
     #[inline]
-    fn chrom(&self) -> &str {
+    pub fn chrom(&self) -> &str {
         &self.chrom
     }
 
     #[inline]
-    fn value(&self, f: Field) -> Result<Value, FieldError> {
+    pub fn value(&self, f: Field) -> Result<Value, FieldError> {
         match f {
             Field::String(name) => match self.fields.get(&name) {
                 None => Err(FieldError::InvalidFieldName(name)),

src/position.rs

@@ -65,9 +65,9 @@ pub enum Position {
     Other(Box<dyn Positioned>),
 }
 
-impl Positioned for Position {
+impl Position {
     #[inline]
-    fn chrom(&self) -> &str {
+    pub fn chrom(&self) -> &str {
         match self {
             Position::Bed(b) => b.chrom(),
             Position::Vcf(v) => v.chrom(),
@@ -78,7 +78,7 @@ impl Positioned for Position {
     }
 
     #[inline]
-    fn start(&self) -> u64 {
+    pub fn start(&self) -> u64 {
         match self {
             Position::Bed(b) => b.start(),
             Position::Vcf(v) => v.start(),
@@ -89,7 +89,7 @@ impl Positioned for Position {
     }
 
     #[inline]
-    fn stop(&self) -> u64 {
+    pub fn stop(&self) -> u64 {
         match self {
             Position::Bed(b) => b.stop(),
             Position::Vcf(v) => v.stop(),
@@ -100,7 +100,7 @@ impl Positioned for Position {
     }
 
     #[inline]
-    fn value(&self, f: Field) -> result::Result<Value, FieldError> {
+    pub fn value(&self, f: Field) -> result::Result<Value, FieldError> {
         match self {
             Position::Bed(b) => b.value(f),
             Position::Vcf(v) => v.value(f),
@@ -155,6 +155,6 @@ pub trait PositionedIterator {
     /// returned position (Positioned equal to previously returned position should have already been returned).
     fn next_position(
         &mut self,
-        q: Option<&dyn Positioned>,
+        q: Option<&Position>,
     ) -> Option<std::result::Result<Position, io::Error>>;
 }