g

src/lib.rs

@@ -128,7 +128,7 @@ pub fn get_n_start_end_qual(
     chr: &str,
     start: i32,
     stop: i32,
-    mapq: u8
+    mapq: u8,
 ) -> Result<usize> {
     bam.fetch((chr, start, stop))?;
 
@@ -138,7 +138,7 @@ pub fn get_n_start_end_qual(
         let record = read.context(format!("eRR"))?;
         let rstart = record.pos() as i32;
         let rend = record.reference_end() as i32;
-        if rstart >= start && rstart < stop  || rend >= start && rend < stop {
+        if rstart >= start && rstart < stop || rend >= start && rend < stop {
             if record.mapq() >= mapq {
                 n_start += 1;
             }
@@ -146,9 +146,43 @@ pub fn get_n_start_end_qual(
     }
 
     Ok(n_start)
-    // Ok(start_positions.len())
 }
 
+pub fn get_start_end_qual(
+    bam: &mut rust_htslib::bam::IndexedReader,
+    chr: &str,
+    start: i32,
+    stop: i32,
+    mapq: u8,
+) -> Result<Vec<i32>> {
+    bam.fetch((chr, start, stop))?;
+    let length = stop - start;
+    let mut results = Vec::new();
+    results.resize(length as usize, 0);
+
+    for read in bam.records() {
+        let record = read.context(format!("Error while parsing record"))?;
+        let rstart = record.pos() as i32;
+        let rend = record.reference_end() as i32;
+
+        if rstart >= start && rstart < stop {
+            if record.mapq() >= mapq {
+                let index = rstart - start;
+                *results.get_mut(index as usize).unwrap() += 1;
+            }
+        }
+
+        if rend >= start && rend < stop {
+            if record.mapq() >= mapq {
+                let index = rend - start;
+                *results.get_mut(index as usize).unwrap() += 1;
+            }
+        }
+
+    }
+
+    Ok(results)
+}
 
 pub fn range_depths(
     bam: &mut rust_htslib::bam::IndexedReader,