feat: implementing AssemblyMapper (#7) (#35)

.github/workflows/rust.yml

@@ -100,7 +100,7 @@ jobs:
         uses: actions-rs/tarpaulin@v0.1
         with:
           version: 0.21.0
-          args: "-- --test-threads 1 ${{ matrix.flag }}"
+          args: "-- --test-threads 1"
         env:
           TEST_UTA_DATABASE_URL: postgres://uta_admin:uta_admin@0.0.0.0/uta
           TEST_UTA_DATABASE_SCHEMA: uta_20210129
@@ -112,7 +112,7 @@ jobs:
         uses: actions-rs/cargo@v1
         with:
           command: test
-          args: "--release -- ${{ matrix.flag }}"
+          args: "--release -- --include-ignored"
         env:
           TEST_UTA_DATABASE_URL: postgres://uta_admin:uta_admin@0.0.0.0/uta
           TEST_UTA_DATABASE_SCHEMA: uta_20210129

Cargo.toml

@@ -27,5 +27,6 @@ serde_json = "1.0.93"
 [dev-dependencies]
 csv = "1.2.0"
 env_logger = "0.10.0"
+rstest = "0.16.0"
 serde = { version = "1.0.152", features = ["derive"] }
 test-log = "0.2.11"

README.md

@@ -31,7 +31,7 @@ export TEST_SEQREPO_CACHE_PATH=tests/data/seqrepo_cache.fasta
 ```
 
 When running the tests with `cargo test`, the cache file will be (re-)written.
-Note that you have to use `cargo test --release -- --test-threads 1 --ignored` when writing the cache for enforcing a single test writing to the cache at any time.
+Note that you have to use `cargo test --release -- --test-threads 1 --include-ignored` when writing the cache for enforcing a single test writing to the cache at any time.
 If you don't want to regenerate the cache then you can use the following settings.
 With these settings, the cache will only be read.
 

src/mapper/alignment.rs

@@ -339,7 +339,7 @@ impl Mapper {
             .map_tgt_to_ref(frs, "start", self.config.strict_bounds)?;
         let gre = self
             .cigar_mapper
-            .map_tgt_to_ref(fre, "start", self.config.strict_bounds)?;
+            .map_tgt_to_ref(fre, "end", self.config.strict_bounds)?;
         let (grs_pos, gre_pos) = (grs.pos + self.gc_offset + 1, gre.pos + self.gc_offset + 1);
         let (gs, ge) = (grs_pos + start_offset, gre_pos + end_offset);