fix parsed_bed_file and test #1

genimtools/src/uniwig/mod.rs

@@ -11,35 +11,20 @@ pub fn read_bed_bec(){
 
 }
 
-pub fn parse_bed_file(line: &str) -> Option<(String, i32, i32, Option<String>)> {
+pub fn parse_bed_file(line: &str) -> Option<(String, i32, i32)> {
     // TODO Eventually refactor all bed file parsing to a single shared function
 
-    let mut iter = line.split('\t');
-    let mut ctg: Option<String> = None;
-    let mut st = -1;
-    let mut en = -1;
-    let mut r: Option<String> = None;
-    let mut i = 0;
-
-    let iter = iter.by_ref();
-
-    while let Some(item) = iter.next()  {
-        match i {
-            0 => ctg = Some(item.to_owned()),
-            1 => st = item.parse().unwrap_or(-1),
-            2 => {
-                en = item.parse().unwrap_or(-1);
-                r = iter.next().map(|x| x.to_owned());
-            }
-            _ => break,
-        }
-        i += 1;
-        if i == 3 || iter.next().is_none() {
-            break;
-        }
-    }
-
-    Some((ctg?, st, en, r))
+    let mut fields = line.split('\t');
+    // Get the first field which should be chromosome.
+    let ctg = fields.next()?;
+    // Parse 2nd and 3rd string as integers or return -1 if failure
+    let st = fields.next().and_then(|s| s.parse::<i32>().ok()).unwrap_or(-1);
+    let en = fields.next().and_then(|s| s.parse::<i32>().ok()).unwrap_or(-1);
+
+    // Original code had a remainder of the line, r, but it does not appear to have been used
+    // in any way
+
+    Some((ctg.parse().unwrap(), st, en))
 
 }
 

genimtools/tests/test.rs

@@ -144,12 +144,11 @@ mod tests {
 
         let result = parse_bed_file(&first_line);
 
-        if let Some((ctg, st, en, r)) = result {
+        if let Some((ctg, st, en)) = result {
 
             println!("ctg: {}", ctg);
             println!("st: {}", st);
             println!("en: {}", en);
-            println!("r: {:?}", r);
             assert_eq!(st, 7915738);
         } else {
             println!("Failed to parse BED record");