Fix early return and counting of mismatches with no-calls in barcodes. (#48)

* fix: early return and counting of mismatches when n in barcodes.

Author: theJasonFan

src/bin/commands/demux.rs

@@ -1373,6 +1373,123 @@ mod tests {
         );
     }
 
+    #[test]
+    fn test_demux_with_catchall_barcode() {
+        let tmp = TempDir::new().unwrap();
+        let read_structures = vec![ReadStructure::from_str("7B+T").unwrap()];
+        let s1_barcode = "NNNNNNN";
+        let sample_metadata = metadata_file(&tmp, &[s1_barcode]);
+        let input_files =
+            vec![fastq_file(&tmp, "ex", "ex", &[&(s1_barcode.to_owned() + &"A".repeat(100))])];
+
+        let output_dir = tmp.path().to_path_buf().join("output");
+
+        let demux_inputs = Demux {
+            inputs: input_files,
+            read_structures,
+            sample_metadata,
+            output_types: vec!['T'],
+            output: output_dir.clone(),
+            unmatched_prefix: "unmatched".to_owned(),
+            max_mismatches: 0,
+            min_mismatch_delta: 2,
+            threads: 5,
+            compression_level: 5,
+            skip_reasons: vec![],
+        };
+        demux_inputs.execute().unwrap();
+
+        let unmatched_path = output_dir.join("unmatched.R1.fq.gz");
+        let unmatched_reads = read_fastq(&unmatched_path);
+        assert_eq!(unmatched_reads.len(), 0);
+
+        let output_path = output_dir.join("Sample0000.R1.fq.gz");
+        let fq_reads = read_fastq(&output_path);
+
+        assert_eq!(fq_reads.len(), 1);
+        assert_equal(
+            &fq_reads[0],
+            &OwnedRecord {
+                head: b"ex_0 1:N:0:NNNNNNN".to_vec(),
+                seq: "A".repeat(100).as_bytes().to_vec(),
+                qual: ";".repeat(100).as_bytes().to_vec(),
+            },
+        );
+    }
+
+    #[test]
+    fn test_demux_with_ns_in_barcode() {
+        let tmp = TempDir::new().unwrap();
+        let read_structures = vec![ReadStructure::from_str("7B+T").unwrap()];
+        let s1_barcode = "NNAAAAA";
+        let s2_barcode = "NNCCCCC";
+        let sample_metadata = metadata_file(&tmp, &[s1_barcode, s2_barcode]);
+        let input_files = vec![fastq_file(
+            &tmp,
+            "ex",
+            "ex",
+            &[
+                &("ANAAAAA".to_owned() + &"A".repeat(5)),
+                &("ANCCCCC".to_owned() + &"C".repeat(5)),
+                &("NNNAAAA".to_owned() + &"T".repeat(5)),
+            ],
+        )];
+
+        let output_dir = tmp.path().to_path_buf().join("output");
+
+        let demux_inputs = Demux {
+            inputs: input_files,
+            read_structures,
+            sample_metadata,
+            output_types: vec!['T'],
+            output: output_dir.clone(),
+            unmatched_prefix: "unmatched".to_owned(),
+            max_mismatches: 0,
+            min_mismatch_delta: 0,
+            threads: 5,
+            compression_level: 5,
+            skip_reasons: vec![],
+        };
+        demux_inputs.execute().unwrap();
+
+        let output_path = output_dir.join("Sample0000.R1.fq.gz");
+        let fq_reads = read_fastq(&output_path);
+        assert_eq!(fq_reads.len(), 1);
+        assert_equal(
+            &fq_reads[0],
+            &OwnedRecord {
+                head: b"ex_0 1:N:0:ANAAAAA".to_vec(),
+                seq: "A".repeat(5).as_bytes().to_vec(),
+                qual: ";".repeat(5).as_bytes().to_vec(),
+            },
+        );
+
+        let output_path = output_dir.join("Sample0001.R1.fq.gz");
+        let fq_reads = read_fastq(&output_path);
+        assert_eq!(fq_reads.len(), 1);
+        assert_equal(
+            &fq_reads[0],
+            &OwnedRecord {
+                head: b"ex_1 1:N:0:ANCCCCC".to_vec(),
+                seq: "C".repeat(5).as_bytes().to_vec(),
+                qual: ";".repeat(5).as_bytes().to_vec(),
+            },
+        );
+
+        // Should not match since it has 3 no calls, and barcodes have at maximum 1 no-call
+        let unmatched_path = output_dir.join("unmatched.R1.fq.gz");
+        let unmatched_reads = read_fastq(&unmatched_path);
+        assert_eq!(unmatched_reads.len(), 1);
+        assert_equal(
+            &unmatched_reads[0],
+            &OwnedRecord {
+                head: b"ex_2 1:N:0:NNNAAAA".to_vec(),
+                seq: "T".repeat(5).as_bytes().to_vec(),
+                qual: ";".repeat(5).as_bytes().to_vec(),
+            },
+        );
+    }
+
     #[test]
     fn test_demux_paired_reads_with_in_line_sample_barcodes() {
         let tmp = TempDir::new().unwrap();

src/lib/barcode_matching.rs

@@ -25,6 +25,8 @@ pub struct BarcodeMatcher {
     /// Note - this is to be replaced by a sample struct in task 3. For now we're keeping things
     /// very simple.
     sample_barcodes: Vec<BString>,
+    /// The maxium number of Ns in any barcode in set of sample barcodes
+    max_ns_in_barcodes: usize,
     /// The maximum mismatches to match a sample barcode.
     max_mismatches: u8,
     /// The minimum difference between number of mismatches in the best and second best barcodes
@@ -56,12 +58,20 @@ impl BarcodeMatcher {
             "Sample barcode cannot be empty string"
         );
 
+        let mut max_ns_in_barcodes = 0;
         let modified_sample_barcodes = sample_barcodes
             .iter()
-            .map(|barcode| BString::from(barcode.to_ascii_uppercase()))
+            .map(|barcode| {
+                let barcode = BString::from(barcode.to_ascii_uppercase());
+                let num_ns = barcode.iter().filter(|&b| byte_is_nocall(*b)).count();
+                max_ns_in_barcodes = max_ns_in_barcodes.max(num_ns);
+                barcode
+            })
             .collect::<Vec<_>>();
+
         Self {
             sample_barcodes: modified_sample_barcodes,
+            max_ns_in_barcodes,
             max_mismatches,
             min_mismatch_delta,
             use_cache,
@@ -132,7 +142,7 @@ impl BarcodeMatcher {
             return None;
         }
         let num_no_calls = read_bases.iter().filter(|&&b| byte_is_nocall(b)).count();
-        if num_no_calls > self.max_mismatches as usize {
+        if num_no_calls > (self.max_mismatches as usize) + self.max_ns_in_barcodes {
             None
         } else if self.use_cache {
             if let Some(cached_match) = self.cache.get(read_bases) {
@@ -207,6 +217,11 @@ mod tests {
         assert_eq!(BarcodeMatcher::count_mismatches("GATTACA".as_bytes(), "GANNACA".as_bytes()), 0,);
     }
 
+    #[test]
+    fn all_ns_barcode_have_no_mismatches() {
+        assert_eq!(BarcodeMatcher::count_mismatches("GANNACA".as_bytes(), "NNNNNNN".as_bytes()), 0,);
+    }
+
     #[test]
     fn find_two_mismatches() {
         assert_eq!(BarcodeMatcher::count_mismatches("GATTACA".as_bytes(), "GACCACA".as_bytes()), 2,);