add simple test for read_bed_vec, check if bed file is gzipped #1

genimtools/src/uniwig/mod.rs

@@ -3,6 +3,8 @@ use std::io::{BufRead, BufReader, Read};
 use std::path::Path;
 use std::fs::{File};
 use std::error::Error;
+use clap::builder::OsStr;
+use flate2::read::GzDecoder;
 
 
 pub mod cli;
@@ -37,6 +39,23 @@ pub fn read_bed_map(combinedbedpath: &str){
 
 pub fn read_bed_vec(combinedbedpath: &str) -> Vec<Chromosome> {
 
+    let path = Path::new(combinedbedpath);
+
+    let file = File::open(path).unwrap();
+
+    let is_gzipped = path.extension().unwrap_or(&OsStr::from("bed")) == "gz";
+
+    if is_gzipped {
+        let decoder = GzDecoder::new(file);
+        let reader = BufReader::new(decoder);
+    }  else {
+        let reader = BufReader::new(file);
+    }
+
+
+
+
+
 
     let chr1 = Chromosome{
         chrom: "".to_string(),

genimtools/tests/test.rs

@@ -31,6 +31,7 @@ fn path_to_tokenize_bed_file() -> &'static str {
 
 mod tests {
     use genimtools::common::utils::extract_regions_from_bed_file;
+    use genimtools::uniwig::read_bed_vec;
 
     use super::*;
 
@@ -155,4 +156,12 @@ mod tests {
         }
 
     }
+
+    #[rstest]
+    fn test_read_bed_vec(path_to_bed_file: &str, path_to_bed_file_gzipped: &str) {
+
+        read_bed_vec(path_to_bed_file);
+        read_bed_vec(path_to_bed_file_gzipped);
+
+    }
 }