Cannot open SAM file with bam::Reader

[holtgrewe]

It forces the file format to be BAM or CRAM.

[vsoch]

heyo! I'm relatively new to rust and I'm hoping this is something I could try helping with. I've been able to clone recursively and run tests (all pass) and then I added a basic test for this case (is this what you are reporting to fail?)

    #[test]
    fn test_read_against_sam() {
        let mut bam = bam::Reader::from_path("./test/bam2sam_out.sam").unwrap();
        for read in bam.records() {
            let read = read.unwrap();
        }
    }

and then it fails.

    Finished test [unoptimized + debuginfo] target(s) in 0.10s
     Running target/debug/deps/rust_htslib-d59cbe136cb7cea4

running 1 test
test bam::ext::tests::test_read_against_sam ... FAILED

failures:

---- bam::ext::tests::test_read_against_sam stdout ----
thread 'bam::ext::tests::test_read_against_sam' panicked at 'called `Result::unwrap()` on an `Err` value: Open { target: "./test/bam2sam_out.sam" }', src/bam/ext.rs:9126:23
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

Could you (or maybe @brainstorm can help) walk through the steps we should take to fix this? Just be safe to assume I know nothing :)

[holtgrewe]

Hi, I think the point to start with would be here.

https://github.com/rust-bio/rust-htslib/blob/master/src/bam/mod.rs#L831

[brainstorm]

Hey @vsoch!

I would start by getting your VSCode up and running with rust-analyzer, since it makes navigating and interacting with Rust projects a bit easier (IMHO), this pack of extensions is quite handy:

https://marketplace.visualstudio.com/items?itemName=jrobsonchase.rust-extension-pack

You were totally in the right path (thanks Manuel!) except the bam:: prefix for the Reader:

diff --git a/src/bam/mod.rs b/src/bam/mod.rs
index 1c7feef..76c622c 100644
--- a/src/bam/mod.rs
+++ b/src/bam/mod.rs
@@ -776,7 +776,8 @@ fn hts_open(path: &[u8], mode: &[u8]) -> Result<*mut htslib::htsFile> {
             unsafe {
                 // Comparison against 'htsFormatCategory_sequence_data' doesn't handle text files correctly
                 // hence the explicit checks against all supported exact formats
-                if (*ret).format.format != htslib::htsExactFormat_bam
+                if (*ret).format.format != htslib::htsExactFormat_sam
+                    && (*ret).format.format != htslib::htsExactFormat_bam
                     && (*ret).format.format != htslib::htsExactFormat_cram
                 {
                     return Err(Error::Open {
@@ -1103,6 +1104,14 @@ CCCCCCCCCCCCCCCCCCC"[..],
         assert_eq!(header_text, true_header);
     }

+    #[test]
+    fn test_read_against_sam() {
+        let mut bam = Reader::from_path("./test/bam2sam_out.sam").unwrap();
+        for read in bam.records() {
+            let _read = read.unwrap();
+        }
+    }
+
     fn _test_read_indexed_common(mut bam: IndexedReader) {
         let (names, flags, seqs, quals, cigars) = gold();
         let sq_1 = b"CHROMOSOME_I";

So please, ship it in the shape of a PR and welcome to the Bio rustaceans shore ;)