Fix bug in get_orientation

rrwick · Jan 11, 2024 · dfad550 · dfad550
1 parent 590d455
commit dfad550
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Showing 2 changed files with 20 additions and 18 deletions.
diff --git a/src/alignment.rs b/src/alignment.rs
@@ -16,6 +16,7 @@ use crate::misc::{quit_with_error, reverse_complement};
 use crate::pileup::Pileup;
 
 use std::collections::HashMap;
+use std::fmt;
 use std::fs::File;
 use std::io;
 use std::io::{prelude::*, BufReader};
@@ -203,6 +204,14 @@ impl Alignment {
     }
 }
 
+impl fmt::Display for Alignment {
+    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
+        let strand = if self.is_on_forward_strand() { "+" } else { "-" };
+        write!(f, "{}:{}{}:{}-{}",
+               self.read_name, self.ref_name, strand, self.ref_start, self.get_ref_end())
+    }
+}
+
 
 pub fn process_sam(filename: &PathBuf, pileups: &mut HashMap<String, Pileup>,
                    max_errors: u32) -> (usize, usize, usize) {

diff --git a/src/filter.rs b/src/filter.rs
@@ -179,31 +179,24 @@ fn get_insert_size_thresholds(alignments: &HashMap<String, Vec<Alignment>>,
 }
 
 
-fn get_orientation(alignment_1: &Alignment, alignment_2: &Alignment) -> String {
-    let strand_1 = if alignment_1.is_on_forward_strand() { 'f' } else { 'r' };
-    let strand_2 = if alignment_2.is_on_forward_strand() { 'f' } else { 'r' };
+fn get_orientation(a_1: &Alignment, a_2: &Alignment) -> String {
+    let strand_1 = if a_1.is_on_forward_strand() { 'f' } else { 'r' };
+    let strand_2 = if a_2.is_on_forward_strand() { 'f' } else { 'r' };
+
+    // Get the read start positions, which is the ref-end position if on the negative strand.
+    let a_1_pos = if a_1.is_on_forward_strand() { a_1.ref_start } else { a_1.get_ref_end() };
+    let a_2_pos = if a_2.is_on_forward_strand() { a_2.ref_start } else { a_2.get_ref_end() };
+
     match (strand_1, strand_2) {
         ('f', 'r') | ('r', 'f') => {
-            if alignment_1.ref_start < alignment_2.ref_start {
+            if a_1_pos < a_2_pos {
                 format!("{}{}", strand_1, strand_2)
             } else {
                 format!("{}{}", strand_2, strand_1)
             }
         },
-        ('f', 'f') => {
-            if alignment_1.ref_start < alignment_2.ref_start {
-                "ff".to_string()
-            } else {
-                "rr".to_string()
-            }
-        },
-        ('r', 'r') => {
-            if alignment_2.ref_start < alignment_1.ref_start {
-                "ff".to_string()
-            } else {
-                "rr".to_string()
-            }
-        },
+        ('f', 'f') => { if a_1_pos < a_2_pos { "ff".to_string() } else { "rr".to_string() } },
+        ('r', 'r') => { if a_2_pos < a_1_pos { "ff".to_string() } else { "rr".to_string() } },
         _ => unreachable!()
     }
 }