Reverse dna read buffer for correct r1/r2 order post-sorting

src/parse/sorted_bam_reader.rs

@@ -113,8 +113,6 @@ impl SortedBamReader {
                 let read1_qname = self.dna_sorted_buffer[i].qname();
                 let read2_qname = self.dna_sorted_buffer[i + 1].qname();
                 if read1_qname == read2_qname {
-                    //paired_reads_buffer.push(self.dna_sorted_buffer[i].clone());
-                    //paired_reads_buffer.push(self.dna_sorted_buffer[i + 1].clone());
                     if self.dna_sorted_buffer[i].is_first_in_template() {
                         paired_reads_buffer.push(self.dna_sorted_buffer[i].clone());
                         paired_reads_buffer.push(self.dna_sorted_buffer[i + 1].clone());
@@ -123,25 +121,6 @@ impl SortedBamReader {
                         paired_reads_buffer.push(self.dna_sorted_buffer[i].clone());
                     }
 
-                    /*println!("first: len: {}", self.dna_sorted_buffer[i].seq_len());
-                    println!("second: len: {}", self.dna_sorted_buffer[i + 1].seq_len());
-                    println!(
-                        "first: first in template: {}",
-                        self.dna_sorted_buffer[i].is_first_in_template()
-                    );
-                    println!(
-                        "first: second in template: {}",
-                        self.dna_sorted_buffer[i].is_last_in_template()
-                    );
-                    println!(
-                        "second: first in template: {}",
-                        self.dna_sorted_buffer[i + 1].is_first_in_template()
-                    );
-                    println!(
-                        "second: second in template: {}\n",
-                        self.dna_sorted_buffer[i + 1].is_last_in_template()
-                    );*/
-
                     seen_qnames.insert(read1_qname);
                     i += 2;
                 } else {
@@ -170,6 +149,7 @@ impl SortedBamReader {
             None => {
                 self.fill_buffer();
                 self.filter_paired_reads();
+                self.dna_sorted_buffer.reverse();
             }
         }