Change circleci script

.circleci/config.yml

@@ -12,17 +12,23 @@ jobs:
       - 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 install cargo-tarpaulin
+      - 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:
             - "~/.cargo"
             - "./target"
+      - run: cargo tarpaulin --out Xml
+      - run: cargo tarpaulin --out Xml -r minimap2-sys
+      - run: bash <(curl -s https://codecov.io/bash)
       - run: cargo test
       - run: cargo test --features htslib
       - run: cargo test --features mm2-fast

.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 --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

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