diff --git a/src/commands/base_depth.rs b/src/commands/base_depth.rs index 040cc86..6715caf 100644 --- a/src/commands/base_depth.rs +++ b/src/commands/base_depth.rs @@ -18,7 +18,7 @@ use structopt::{StructOpt, clap::AppSettings}; /// Calculate the depth at each base, per-nucleotide. #[derive(StructOpt)] -#[structopt(author, global_settings = &[AppSettings::ArgRequiredElseHelp])] +#[structopt(author, setting = AppSettings::ArgRequiredElseHelp)] pub struct BaseDepth { /// Input indexed BAM/CRAM to analyze. reads: PathBuf, diff --git a/src/commands/merge_adjacent.rs b/src/commands/merge_adjacent.rs index b9c835f..0a07775 100644 --- a/src/commands/merge_adjacent.rs +++ b/src/commands/merge_adjacent.rs @@ -12,7 +12,7 @@ use structopt::{StructOpt, clap::AppSettings}; /// Generally accepts any file with no header that is \t\t\t. /// The is optional. See documentation for explanation of headers that are accepted. #[derive(StructOpt)] -#[structopt(author, global_settings = &[AppSettings::ArgRequiredElseHelp])] +#[structopt(author, setting = AppSettings::ArgRequiredElseHelp)] pub struct MergeAdjacent { /// Input bed-like file, defaults to STDIN. in_file: Option, diff --git a/src/commands/only_depth.rs b/src/commands/only_depth.rs index bf32869..1033a42 100644 --- a/src/commands/only_depth.rs +++ b/src/commands/only_depth.rs @@ -23,7 +23,7 @@ use structopt::{StructOpt, clap::AppSettings}; /// Calculate only the depth at each base. #[derive(StructOpt)] -#[structopt(author, global_settings = &[AppSettings::ArgRequiredElseHelp])] +#[structopt(author, setting = AppSettings::ArgRequiredElseHelp)] pub struct OnlyDepth { /// Input indexed BAM/CRAM to analyze. reads: PathBuf, diff --git a/src/main.rs b/src/main.rs index 6526321..646510f 100644 --- a/src/main.rs +++ b/src/main.rs @@ -8,7 +8,7 @@ use perbase_lib::utils; use structopt::{StructOpt, clap::AppSettings}; #[derive(StructOpt)] -#[structopt(rename_all = "kebab-case", author, about, global_settings = &[AppSettings::SubcommandRequiredElseHelp])] +#[structopt(rename_all = "kebab-case", author, about, setting = AppSettings::SubcommandRequiredElseHelp)] /// Commands for generating per-base analysis struct Args { #[structopt(subcommand)]