diff --git a/Cargo.toml b/Cargo.toml index c40c2dd..c8fcea2 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -26,11 +26,11 @@ zip = { version = "0.6", default-features = false, features=["deflate"] } byteorder = "1" serde = { version = "1.0", features = ["derive"] } serde_json = "1.0" -json5 = "*" fasteval = { version = "0.2.4", features= ["unsafe-vars"]} bincode = { version = "1.3.3" } +json5 = "0.4.1" [profile.release] lto = "fat" diff --git a/src/main.rs b/src/main.rs index 4c2f2f1..2ec7f39 100644 --- a/src/main.rs +++ b/src/main.rs @@ -25,8 +25,8 @@ fn main() -> Result<(), Box> { (about: "annotate a VCF/BCF with one or more echtvar files") (@arg echtvar: -e + takes_value number_of_values(1) ... "echtvar files to annotate with. can be specified many times") (@arg include: -i +takes_value number_of_values(1) "expression that determines which variants to keep in output") - (@arg INPUT_VCF: +required "vcf") - (@arg OUTPUT_VCF: +required "path to bcf output file") + (@arg INPUT_VCF: +required "input vcf or bcf") + (@arg OUTPUT_VCF: +required "path to bcf/vcf.gz output file (determined by extension)") ) ); let matches = app.clone().get_matches();