Merge pull request #14 from esteinig/bam_reader

Bam reader

.pre-commit-config.yaml

@@ -0,0 +1,5 @@
+repos:
+  - repo: https://github.com/doublify/pre-commit-rust
+    rev: v1.0
+    hooks:
+      - id: fmt

Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 rust-version = "1.58"
 name = "vircov"
-version = "0.3.0"
+version = "0.4.0"
 authors = ["esteinig <[email protected]>"]
 description = "Vircov: genome coverage assessment for viral metagenomic diagnostics"
 documentation = "https://github.com/esteinig/vircov"
@@ -19,17 +19,17 @@ include = [
 ]
 
 [dependencies]
-csv = "1.1"
+bio = "0.40"
 anyhow = "1.0"
 clap = "2.33.0"
 tabled = "0.5.0"
 structopt = "0.3"
 thiserror = "1.0"
 crossterm = "0.23.0"
 itertools = "0.10.3"
+rust-htslib = "0.38"
 rust-lapper = "1.0.0"
-serde = { version = "1.0.136", features = ["derive"] }
-noodles = { version = "0.20.0", features = ["fasta"] }
+
 
 [dev-dependencies]
 assert_cmd = "2.0.1"

codecov.yaml

@@ -0,0 +1,24 @@
+codecov:
+  require_ci_to_pass: true # Should Codecov wait for all other statues to pass before sending it's status.
+
+coverage:
+  precision: 2
+  round: up
+  range: "75...100"  # The value range where you want the value to be green
+
+parsers:
+  gcov:
+    branch_detection:
+      conditional: yes
+      loop: yes
+      method: no
+      macro: no
+
+comment:
+  layout: "reach, diff, flags, files"
+  behavior: default
+  require_changes: false  # if true: only post the comment if coverage changes
+  require_base: no        # [yes :: must have a base report to post]
+  require_head: yes       # [yes :: must have a head report to post]
+  branches:               # branch names that can post comment
+    - "main"