g

src/lib.rs

@@ -1,7 +1,7 @@
 use anyhow::{Context, Ok, Result};
 use rust_htslib::{
     bam,
-    bam::{ext::BamRecordExtensions, record, Read},
+    bam::{ext::BamRecordExtensions, record, Read, Record},
 };
 
 use average::Mean;
@@ -178,12 +178,51 @@ pub fn get_start_end_qual(
                 *results.get_mut(index as usize).unwrap() += 1;
             }
         }
-
     }
 
     Ok(results)
 }
 
+pub fn get_start_end_qual_rec(
+    bam: &mut rust_htslib::bam::IndexedReader,
+    chr: &str,
+    start: i32,
+    stop: i32,
+    mapq: u8,
+) -> Result<Vec<Vec<Record>>> {
+    bam.fetch((chr, start, stop))?;
+    let length = stop - start;
+    let mut results: Vec<Vec<Record>> = Vec::new();
+    results.resize(length as usize, vec![]);
+
+    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()
+                    .push(record.clone());
+            }
+        }
+
+        if rend >= start && rend < stop {
+            if record.mapq() >= mapq {
+                let index = rend - start;
+                results
+                    .get_mut(index as usize)
+                    .unwrap()
+                    .push(record.clone());
+            }
+        }
+    }
+    Ok(results)
+}
+
 pub fn range_depths(
     bam: &mut rust_htslib::bam::IndexedReader,
     chr: &str,