fix(main): fix command line argument parsing bug

cauliyang · Nov 1, 2023 · eaf1428 · eaf1428
1 parent de38bf4
commit eaf1428
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Showing 3 changed files with 3 additions and 4 deletions.
diff --git a/Cargo.toml b/Cargo.toml
@@ -26,12 +26,13 @@ codegen-units = 1
 
 [dependencies]
 anyhow = { version = "1.0" }
-clap = { version = "4.4.7", features = ["wrap_help", "derive"] }
+clap = { version = "4.4.7", features = ["wrap_help", "derive", "color"] }
 clap-verbosity-flag = "2.1.0"
 env_logger = "0.10"
 human-panic = "1.2.1"
 indicatif = "0.17"
 log = "0.4"
+colored = "2"
 
 noodles-bam = "0.49.0"
 noodles-bgzf = "0.25"

diff --git a/src/extract.rs b/src/extract.rs
@@ -39,7 +39,6 @@ where
             ReadName::try_from(s.into_bytes())
                 .map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
         })?;
-
         read_names.insert(read_name);
     }
 

diff --git a/src/main.rs b/src/main.rs
@@ -22,12 +22,11 @@ enum Commands {
     /// Extract reads from a BAM file
     Extract {
         /// Read IDs
-        #[arg(short, long)]
         readids: String,
         /// Bam input file
-        #[arg(short, long)]
         input: PathBuf,
 
+        /// Is the output file a BAM file
         #[arg(short = 'b', default_value = "false")]
         isbam: bool,
     },