Merge branch 'main' of https://github.com/ebioman/AgnosticBamCounter

.devcontainer/devcontainer.json

@@ -0,0 +1,31 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/rust
+{
+	"name": "Rust",
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"image": "mcr.microsoft.com/devcontainers/rust:0-1-bullseye",
+
+	// Use 'mounts' to make the cargo cache persistent in a Docker Volume.
+	// "mounts": [
+	// 	{
+	// 		"source": "devcontainer-cargo-cache-${devcontainerId}",
+	// 		"target": "/usr/local/cargo",
+	// 		"type": "volume"
+	// 	}
+	// ]
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	"postCreateCommand": "sudo apt-get update && sudo apt-get install -y  cmake"
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

Cargo.toml

@@ -2,7 +2,6 @@
 name    = "abc"
 version = "0.3.3"
 authors = ["Emanuel Schmid-Siegert"]
-edition = "2018"
 description   =  """
 The Agnostic Bam Counter (abc) determines at a given positions the count of observed nucleotides.
 Simply supply a bed file with positions and obtains a tsv file with counts for each ATCG and reference if provided.
@@ -18,16 +17,14 @@ Note:
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [dependencies]
-rust-htslib = { version = "*", default-features = false }
+rust-htslib = "0.40.2"
 #regex = "1"
-log = "0.4"
-env_logger = "0.9.3"
-clap = "*"
-csv = "*"
-chrono = "*"
-bio = "*"
+clap = "4.1.6"
+csv = "1.2.0"
+chrono = "0.4.23"
+bio = "1.1.0"
 itertools = "*"
 bambam = {git = "https://github.com/ebioman/bambam"}
-crossbeam = "*"
-crossbeam-channel = "*"
-rayon = "*"
+crossbeam = "0.8.2"
+crossbeam-channel = "0.5.6"
+rayon = "1.6.1"