feat: transcript based annotation (#11) (#14)

.gitattributes

@@ -1 +1,4 @@
 tests/data/db/create/txs/latest/** filter=lfs diff=lfs merge=lfs -text
+tests/data/vars/*.vcf*
+tests/data/vars/*.tsv*
+*.bin filter=lfs diff=lfs merge=lfs -text

.github/workflows/rust.yml

@@ -65,6 +65,12 @@ jobs:
     needs: Formatting
     runs-on: ubuntu-latest
 
+    strategy:
+      matrix:
+        include:
+          - label: fast
+          - label: full
+
     services:
       # The tests need a postgres server;  the data will be loaded later
       # after checkout.
@@ -109,10 +115,19 @@ jobs:
         with:
           version: 0.21.0
           args: "-- --test-threads 1"
+        if: ${{ matrix.label == 'fast' }}
+
+      - name: Run cargo-tarpaulin with full tests
+        uses: actions-rs/[email protected]
+        with:
+          version: 0.21.0
+          args: "--release --timeout=180 -- --include-ignored"
+        if: ${{ matrix.label == 'full' }}
 
       - name: Codecov submission of fast test results
         uses: codecov/codecov-action@v3
         with:
           verbose: true
           fail_ci_if_error: true
           token: ${{ secrets.CODECOV_TOKEN }}
+        if: ${{ matrix.label == 'fast' }}

.gitignore

@@ -1,6 +1,8 @@
 /target
 #/Cargo.lock
 
+*:Zone.Identifier
+
 *~
 .*.sw?
 /.vscode

Cargo.toml

@@ -20,7 +20,9 @@ clap-verbosity-flag = "2.0.0"
 csv = "1.2.0"
 flatbuffers = "23.1.21"
 flate2 = "1.0.25"
-hgvs = "0.3.1"
+#hgvs = { git = "https://github.com/bihealth/hgvs-rs.git", branch = "main" }
+#hgvs = { path = "/home/holtgrem_c/Development/hgvs-rs" }
+hgvs = "0.4.0"
 lazy_static = "1.4.0"
 log = "0.4.17"
 noodles = { version = "0.33.0", features = ["vcf", "bcf", "csi", "fasta", "bgzf", "tabix"] }
@@ -34,10 +36,17 @@ tracing = { version = "0.1.37", features = ["log"] }
 tracing-subscriber = "0.3.16"
 indicatif = "0.17.3"
 thousands = "0.2.0"
+memmap2 = "0.5.10"
+bio = "1.1.0"
+parse-display = "0.8.0"
+nom = "7.1.3"
+linked-hash-map = "0.5.6"
+enumset = { version = "1.0.12", features = ["serde"] }
 
 [build-dependencies]
 flatc-rust = "0.2.0"
 
 [dev-dependencies]
+csv = "1.2.0"
 pretty_assertions = "1.3.0"
 temp_testdir = "0.2.3"