back to working example

examples/intersect.rs

@@ -59,20 +59,19 @@ struct Args {
 fn main() -> io::Result<()> {
     let args = Args::parse();
 
-    let a = bedder::sniff::HtsFile::new(&args.a, "r").expect("Failed to open file");
-
-    let ai = a.into();
+    let a = BufReader::new(fs::File::open(&args.a)?);
+    let ai = bedder::sniff::open(a, &args.a)?;
 
     //let ai = sniff::open_file(&args.a)?;
     let bis = args
         .b
         .iter()
         .map(|b| {
-            bedder::sniff::HtsFile::new(b, "r")
-                .expect("Failed to open file")
-                .into()
+            let f = BufReader::new(fs::File::open(b)?);
+            let b = bedder::sniff::open(f, b)?;
+            Ok(b.into_positioned_iterator())
         })
-        .collect::<Vec<Box<dyn bedder::position::PositionedIterator>>>();
+        .collect::<io::Result<Vec<Box<dyn bedder::position::PositionedIterator>>>>()?;
 
     // bedder always requires a hashmap that indicates the chromosome order
 
@@ -94,6 +93,11 @@ fn main() -> io::Result<()> {
         }
     };
 
+    let ai = match ai {
+        bedder::sniff::BedderReader::BedderBed(rdr) => rdr,
+        _ => unimplemented!(),
+    };
+
     // we can have any number of b (other_iterators).
     let it = IntersectionIterator::new(ai, bis, &h)?;
 
@@ -148,7 +152,9 @@ fn main() -> io::Result<()> {
         }
         //eprintln!("report: {:?}", report);
         //eprintln!("args: {:?}", &args);
-        let columns = ["chrom", "start", "stop", "a_id", "b_id", "a_count", "b_count"];
+        let columns = [
+            "chrom", "start", "stop", "a_id", "b_id", "a_count", "b_count",
+        ];
         //let c = ColumnReporter::new();
         let v = vec![];
 

src/sniff.rs

@@ -1,6 +1,9 @@
+use crate::bedder_bed::BedderBed;
+use crate::position::PositionedIterator;
 use flate2::bufread::GzDecoder;
-use std::io;
-use std::io::Read;
+use std::fs::File;
+use std::io::{self, Read};
+use std::path::Path;
 
 #[derive(Debug)]
 pub enum FileType {
@@ -17,7 +20,40 @@ pub enum Compression {
     None,
 }
 
+pub enum BedderReader<R>
+where
+    R: io::BufRead + io::Seek + 'static,
+{
+    BedderBed(BedderBed<'static, R>),
+}
+
+impl<R> BedderReader<R>
+where
+    R: io::BufRead + io::Seek + 'static,
+{
+    pub fn new<P: AsRef<Path>>(reader: R, path: P) -> io::Result<Self> {
+        open(reader, path)
+    }
+
+    pub fn into_positioned_iterator(self) -> Box<dyn PositionedIterator> {
+        match self {
+            BedderReader::BedderBed(rdr) => Box::new(rdr),
+        }
+    }
+}
 // TODO: https://github.com/quinlan-lab/bedder-rs/blob/ffddd2b3a2075594a5375fb81b8672f4f5039acf/src/sniff.rs
+pub fn open<P: AsRef<Path>, R: io::BufRead + io::Seek + 'static>(
+    mut reader: R,
+    p: P,
+) -> io::Result<BedderReader<R>> {
+    let (ft, c) =
+        sniff(&mut reader).map_err(|e| io::Error::new(io::ErrorKind::Other, e.to_string()))?;
+    let rdr = match ft {
+        FileType::Bed => BedderReader::BedderBed(BedderBed::new(reader, Some(p))),
+        _ => unimplemented!(),
+    };
+    Ok(rdr)
+}
 
 pub fn sniff<R: io::BufRead>(
     rdr: &mut R,