Merge pull request #19 from jguhlin/tests

Some minor tests, change the grcov script to better find coverage

Author: jguhlin

.circleci/config.yml

@@ -5,19 +5,30 @@ version: 2.1
 # Define a job to be invoked later in a workflow.
 # See: https://circleci.com/docs/2.0/configuration-reference/#jobs
 jobs:
+  coverage: 
+    machine: true
+    steps:
+      - checkout
+      - run: docker run --security-opt seccomp=unconfined -v "${PWD}:/volume" xd009642/tarpaulin /bin/bash -c "apt-get update; apt-get install cmake -y; cargo build --features htslib; cargo tarpaulin --features htslib --out Xml"
+      # - run: cargo tarpaulin --out Xml --features htslib,map-file
+      # - run: cargo tarpaulin --out Xml -r minimap2-sys
+      - run: bash <(curl -s https://codecov.io/bash)
+
   test:
     docker:
       - image: cimg/rust:1.65.0
     steps:
       - checkout
       - restore_cache:
           key: project-cache
-      - run: cargo install grcov
-      - run: cargo --version
-      - run: bash .scripts/grcov.bash
-      - run: curl -Os https://uploader.codecov.io/latest/linux/codecov
-      - run: chmod +x codecov
-      - run: ./codecov
+      #- run: cargo install grcov
+      #- run: cargo --version
+      #- run: bash .scripts/grcov.bash
+      - run: cargo build
+      - run: cargo build --features htslib
+      - run: cargo build --features mm2-fast
+      - run: cargo build --features simde
+      - run: cargo build --features htslib,mm2-fast,simde
       - save_cache:
           key: project-cache
           paths:
@@ -40,3 +51,4 @@ workflows:
   minimap2-test:
     jobs:
       - test
+      - coverage

.github/workflows/build-test-rust.yml

@@ -13,21 +13,14 @@ jobs:
     container: messense/rust-musl-cross:x86_64-musl
     steps:
     - uses: actions/checkout@v3
-    - uses: NSCoder/[email protected]
     - name: Build
       run: cargo build --verbose
     - name: Run tests
       run: cargo test
-    - name: Run tests mm2-fast
-      run: cargo test --features mm2-fast
     - name: Run tests htslib
       run: cargo test --features htslib
-    - name: Run tests simde
-      run: cargo test --features simde
-    
 
   test:
-
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3

.scripts/grcov.bash

@@ -7,10 +7,14 @@ export RUSTDOCFLAGS="-Cpanic=abort"
 export LLVM_PROFILE_FILE="sfasta-%p-%m.profraw"
 
 mkdir -p target/coverage
+mkdir -p minimap2-sys/target/coverage
 
-cargo test
+cargo test --features htslib,mm2-fast,simde,map-file
+cd minimap2-sys
+cargo test --features mm2-fast,simde
+cd ..
 
 #grcov . -s . --binary-path ./target/debug/ -t lcov --branch --ignore-not-existing -o ./target/debug/coverage/
 grcov . --binary-path ./target/debug/deps/ -s . -t lcov --branch --ignore-not-existing --ignore '../*' --ignore "/*" -o target/coverage/tests.lcov
-grcov . -s . --binary-path ./target/debug/ -t html --branch --ignore-not-existing -o ./target/debug/coverage/
+# grcov . -s . --binary-path ./target/debug/ -t html --branch --ignore-not-existing -o ./target/debug/coverage/
 #genhtml -o ./target/debug/coverage/ --show-details --highlight --ignore-errors source --legend ./target/debug/lcov.info

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "minimap2"
-version = "0.1.11"
+version = "0.1.12"
 edition = "2021"
 authors = ["Joseph Guhlin <[email protected]>"]
 license = "MIT OR Apache-2.0"

README.md

@@ -103,8 +103,10 @@ let mut aligner = Aligner::builder()
 The following crate features are available:
 * `mm2-fast` - Replace minimap2 with [mm2-fast](https://github.com/bwa-mem2/mm2-fast). This is likely not portable.
 * `htslib` - Support output of bam/sam files using htslib.
-* `map-file` - Convenience function for mapping an entire file. Caution, this is single-threaded.
 * `simde` - Compile minimap2 / mm2-fast with [simd-everywhere](https://github.com/simd-everywhere/simde) support. 
+* `map-file` - *Default* - Convenience function for mapping an entire file. Caution, this is single-threaded. 
+
+Map-file is a *default* feature and enabled unless otherwise specified.
 
 ## Building for MUSL
 Follow these [instructions](https://github.com/rust-cross/rust-musl-cross#prebuilt-images).
@@ -118,6 +120,12 @@ rust-musl-builder cargo build --release
 
 Please note minimap2 is only tested for x86_64. Other platforms may work, please open an issue if minimap2 compiles but minimap2-rs does not.
 
+### Features tested with MUSL
+* `mm2-fast` - **Fail**
+* `htslib` - **Success**
+* `simde` - **Success**
+
+
 # Want feedback
 * Many fields are i32 / i8 to mimic the C environment, but would it make more sense to convert to u32 / u8 / usize?
 * Let me know pain points

minimappers2/pyproject.toml

@@ -17,6 +17,11 @@ dependencies = [
     "pyarrow==10.0.1",
 ]
 
+[project.urls]
+homepage = "https://github.com/jguhlin/minimap2-rs"
+repository = "https://github.com/jguhlin/minimap2-rs"
+
+
 [build-system]
 requires = ["maturin>=0.14,<0.15"]
 build-backend = "maturin"

src/lib.rs

@@ -882,14 +882,14 @@ pub fn detect_compression_format(buffer: &[u8]) -> Result<CompressionType, &'sta
     Ok(match buffer {
         [0x1F, 0x8B, ..] => CompressionType::GZIP,
         [0x42, 0x5A, ..] => CompressionType::BZIP2,
-        [0xFD, b'7', b'z', b'X', b'Z', 0x00] => CompressionType::XZ,
+        [0xFD, b'7', b'z', b'X', b'Z', 0x00, ..] => CompressionType::XZ,
         [0x28, 0xB5, 0x2F, 0xFD, ..] => CompressionType::LZMA,
         [0x5D, 0x00, ..] => CompressionType::LZMA,
         [0x1F, 0x9D, ..] => CompressionType::LZMA,
-        [0x37, 0x7A, 0xBC, 0xAF, 0x27, 0x1C] => CompressionType::ZSTD,
+        [0x37, 0x7A, 0xBC, 0xAF, 0x27, 0x1C, ..] => CompressionType::ZSTD,
         [0x04, 0x22, 0x4D, 0x18, ..] => CompressionType::LZ4,
         [0x08, 0x22, 0x4D, 0x18, ..] => CompressionType::LZ4,
-        [0x52, 0x61, 0x72, 0x21, 0x1A, 0x07] => CompressionType::RAR,
+        [0x52, 0x61, 0x72, 0x21, 0x1A, 0x07, ..] => CompressionType::RAR,
         _ => CompressionType::NONE,
     })
 }
@@ -899,6 +899,34 @@ mod tests {
     use super::*;
     use std::mem::MaybeUninit;
 
+    #[test]
+    fn compression_format_detections() {
+        let buf = [0x1F, 0x8B, 0x08, 0x08, 0x00, 0x00, 0x00, 0x00, 0x00, 0xFF];
+        assert_eq!(detect_compression_format(&buf).unwrap(), CompressionType::GZIP);
+
+        let buf = [0x42, 0x5A, 0x68, 0x39, 0x31, 0x41, 0x59, 0x26, 0x53, 0x59];
+        assert_eq!(detect_compression_format(&buf).unwrap(), CompressionType::BZIP2);
+
+        let buf = [0x28, 0xB5, 0x2F, 0xFD, 0x37, 0x00, 0x00, 0x00, 0x00, 0x00];
+        assert_eq!(detect_compression_format(&buf).unwrap(), CompressionType::LZMA);
+
+        let buf = [0x04, 0x22, 0x4D, 0x18, 0x40, 0x40, 0x00, 0x00, 0x00, 0x00];
+        assert_eq!(detect_compression_format(&buf).unwrap(), CompressionType::LZ4);
+
+        let buf = [0x08, 0x22, 0x4D, 0x18, 0x40, 0x40, 0x00, 0x00, 0x00, 0x00];
+        assert_eq!(detect_compression_format(&buf).unwrap(), CompressionType::LZ4);
+
+        let buf = [0x52, 0x61, 0x72, 0x21, 0x1A, 0x07, 0x00, 0x00, 0x00, 0x00];
+        assert_eq!(detect_compression_format(&buf).unwrap(), CompressionType::RAR);
+
+        let buf = [0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00];
+        assert_eq!(detect_compression_format(&buf).unwrap(), CompressionType::NONE);
+
+        let buf = [0x37, 0x7A, 0xBC, 0xAF, 0x27, 0x1C, 0x00, 0x00, 0x00, 0x00];
+        assert_eq!(detect_compression_format(&buf).unwrap(), CompressionType::ZSTD);
+
+    }
+
     #[test]
     fn does_it_work() {
         let mut mm_idxopt = MaybeUninit::uninit();
@@ -960,6 +988,9 @@ mod tests {
         println!("Reverse Strand\n{:#?}", mappings);
         assert!(mappings[0].strand == Strand::Reverse);
 
+        // Assert the Display impl for strand works
+        println!("{}", mappings[0].strand);
+
         let mut aligner = aligner.with_cigar();
 
         aligner