test: add integration tests for reader-based BAM header parsing

Verify that parse_bam_from_reader correctly handles roundtrip encoding
and truncated streams (partial uploads with trailing garbage).

Author: nh13

tests/header_extraction_tests.rs

@@ -0,0 +1,70 @@
+//! Integration tests for header-only parsing from binary uploads.
+//!
+//! Verifies that the server can parse headers from BAM/CRAM bytes
+//! sent as multipart uploads, including truncated streams.
+
+use std::io::Cursor;
+use std::num::NonZeroUsize;
+
+use noodles::bam;
+use noodles::sam;
+use noodles::sam::header::record::value::map::ReferenceSequence;
+use noodles::sam::header::record::value::Map;
+
+/// Create a minimal BAM file in memory with the given contigs.
+fn create_test_bam(contigs: &[(&str, usize)]) -> Vec<u8> {
+    let mut header = sam::Header::builder();
+    for &(name, length) in contigs {
+        header = header.add_reference_sequence(
+            name,
+            Map::<ReferenceSequence>::new(NonZeroUsize::new(length).unwrap()),
+        );
+    }
+    let header = header.build();
+
+    let mut buf = Vec::new();
+    {
+        let mut writer = bam::io::Writer::new(&mut buf);
+        writer.write_header(&header).unwrap();
+    }
+    buf
+}
+
+#[test]
+fn test_parse_bam_from_reader_roundtrip() {
+    use ref_solver::parsing::sam::parse_bam_from_reader;
+
+    let contigs = [
+        ("chr1", 248_956_422),
+        ("chr2", 242_193_529),
+        ("chr3", 198_295_559),
+        ("chrX", 156_040_895),
+        ("chrY", 57_227_415),
+        ("chrM", 16_569),
+    ];
+
+    let bam_bytes = create_test_bam(&contigs);
+    let cursor = Cursor::new(&bam_bytes);
+    let query = parse_bam_from_reader(cursor).unwrap();
+
+    assert_eq!(query.contigs.len(), contigs.len());
+    for (i, &(name, length)) in contigs.iter().enumerate() {
+        assert_eq!(query.contigs[i].name, name);
+        assert_eq!(query.contigs[i].length, length as u64);
+    }
+}
+
+#[test]
+fn test_parse_bam_from_reader_with_trailing_garbage() {
+    use ref_solver::parsing::sam::parse_bam_from_reader;
+
+    let mut bam_bytes = create_test_bam(&[("chr1", 248_956_422)]);
+    // Simulate a truncated upload — header is complete but record data is garbage.
+    // parse_bam_from_reader only reads the header, so this must still succeed.
+    bam_bytes.extend_from_slice([0xDE, 0xAD, 0xBE, 0xEF].repeat(25).as_slice());
+    let cursor = Cursor::new(&bam_bytes);
+    let query = parse_bam_from_reader(cursor).unwrap();
+
+    assert_eq!(query.contigs.len(), 1);
+    assert_eq!(query.contigs[0].name, "chr1");
+}