From 60c06a151b49cc7ff289673ead93a059b0cd6857 Mon Sep 17 00:00:00 2001
From: Nils Homer <nh13@users.noreply.github.com>
Date: Fri, 9 Jun 2023 11:28:47 -0700
Subject: [PATCH] Do not require comment to have 4 segments (#26)

* Attempt to fix 25
---
 src/bin/commands/demux.rs | 46 +++++++++++++++++++++++----------------
 1 file changed, 27 insertions(+), 19 deletions(-)

diff --git a/src/bin/commands/demux.rs b/src/bin/commands/demux.rs
index d144092..5e69edc 100644
--- a/src/bin/commands/demux.rs
+++ b/src/bin/commands/demux.rs
@@ -190,25 +190,32 @@ impl ReadSet {
                 // Else check it's a 4-part name... fix the read number at the front and
                 // check to see if there's a real sample barcode on the back
                 let sep_count = chars.iter().filter(|c| **c == Self::COLON).count();
-                ensure!(
-                    sep_count == 3,
-                    "Comment in did not have 4 segments: {}",
-                    String::from_utf8(header.to_vec())?
-                );
-                let first_colon_idx = chars.iter().position(|ch| *ch == Self::COLON).unwrap();
-
-                // Illumina, in the unmatched FASTQs, can place a "0" in the index position, sigh
-                let remainder = if chars.last().unwrap().is_ascii_digit() {
-                    &chars[first_colon_idx + 1..chars.len() - 1]
+                if sep_count < 3 {
+                    writer.write_all(chars)?;
+                    if *chars.last().unwrap() != Self::COLON {
+                        writer.write_all(&[Self::COLON])?;
+                    }
                 } else {
-                    &chars[first_colon_idx + 1..chars.len()]
-                };
-
-                write!(writer, "{}:", read_num)?;
-                writer.write_all(remainder)?;
-
-                if *remainder.last().unwrap() != Self::COLON {
-                    writer.write_all(&[Self::PLUS])?;
+                    ensure!(
+                        sep_count == 3,
+                        "Comment in did not have 4 segments: {}",
+                        String::from_utf8(header.to_vec())?
+                    );
+                    let first_colon_idx = chars.iter().position(|ch| *ch == Self::COLON).unwrap();
+
+                    // Illumina, in the unmatched FASTQs, can place a "0" in the index position, sigh
+                    let remainder = if chars.last().unwrap().is_ascii_digit() {
+                        &chars[first_colon_idx + 1..chars.len() - 1]
+                    } else {
+                        &chars[first_colon_idx + 1..chars.len()]
+                    };
+
+                    write!(writer, "{}:", read_num)?;
+                    writer.write_all(remainder)?;
+
+                    if *remainder.last().unwrap() != Self::COLON {
+                        writer.write_all(&[Self::PLUS])?;
+                    }
                 }
             }
         }
@@ -1648,13 +1655,13 @@ mod tests {
     }
 
     #[test]
-    #[should_panic(expected = "4 segments")]
     fn test_write_header_comment_too_few_parts() {
         let mut out = Vec::new();
         let header = b"q1 0:0";
         let barcode_segs =
             [seg(b"ACGT", SegmentType::SampleBarcode), seg(b"GGTT", SegmentType::SampleBarcode)];
         let umi_segs = [seg(b"AACCGGTT", SegmentType::MolecularBarcode)];
+        let expected = "@q1:AACCGGTT 0:0:ACGT+GGTT".to_string();
         ReadSet::write_header_internal(
             &mut out,
             1,
@@ -1663,6 +1670,7 @@ mod tests {
             umi_segs.iter().filter(|_| true),
         )
         .unwrap();
+        assert_eq!(String::from_utf8(out).unwrap(), expected);
     }
 
     // ############################################################################################