fix: bam::Record:new should return a valid record

src/bam/mod.rs

@@ -2818,4 +2818,59 @@ CCCCCCCCCCCCCCCCCCC"[..],
         assert_eq!(header_refseqs[0].get("SN").unwrap(), "ref_1",);
         assert_eq!(header_refseqs[0].get("LN").unwrap(), "10000000",);
     }
+
+    #[test]
+    fn test_bam_new() {
+        // Create the path to write the tmp test BAM
+        let tmp = tempfile::Builder::new()
+            .prefix("rust-htslib")
+            .tempdir()
+            .expect("Cannot create temp dir");
+        let bampath = tmp.path().join("test.bam");
+
+        // write an unmapped BAM record (uBAM)
+        {
+            // Build the header
+            let mut header = Header::new();
+
+            // Add the version
+            header.push_record(
+                HeaderRecord::new(b"HD")
+                    .push_tag(b"VN", &"1.6")
+                    .push_tag(b"SO", &"unsorted"),
+            );
+
+            // Build the writer
+            let mut writer = Writer::from_path(bampath, &header, Format::Bam).unwrap();
+
+            // Build an empty record
+            let mut record = Record::new();
+
+            // By default the read is mapped, so unset it.
+            record.set_unmapped();
+
+            // Write the record (this previously seg-faulted)
+            writer.write(&record);
+        }
+
+        // Read the record
+        {
+            // Build th reader
+            let mut reader = Reader::from_path(&bampath).expect("Error opening file.");
+
+            // Read the record
+            let mut rec = Record::new();
+            match bam.read(&mut rec) {
+                Some(r) => r.expect("Failed to read record."),
+                None => {}
+            };
+
+            // Check a few things
+            assert!(rec.is_unmapped());
+            assert_eq!(rec.tid(), -1);
+            assert_eq!(rec.pos(), -1);
+            assert_eq!(rec.mtid(), -1);
+            assert_eq!(rec.mpos(), -1);
+        }
+    }
 }

src/bam/record.rs

@@ -113,12 +113,19 @@ fn extranul_from_qname(qname: &[u8]) -> usize {
 impl Record {
     /// Create an empty BAM record.
     pub fn new() -> Self {
-        Record {
+        let mut record = Record {
             inner: unsafe { MaybeUninit::zeroed().assume_init() },
             own: true,
             cigar: None,
             header: None,
-        }
+        };
+        // Developer note: these are needed so the returned record is properly
+        // initialized as unmapped.
+        record.set_tid(-1);
+        record.set_pos(-1);
+        record.set_mpos(-1);
+        record.set_mtid(-1);
+        record
     }
 
     pub fn from_inner(from: *mut htslib::bam1_t) -> Self {