From eaf1428f959eac531af6a696e726b52e022b88e4 Mon Sep 17 00:00:00 2001
From: Yangyang Li <yangyang.li@northwestern.edu>
Date: Wed, 1 Nov 2023 11:28:52 -0500
Subject: [PATCH] fix(main): fix command line argument parsing bug

---
 Cargo.toml     | 3 ++-
 src/extract.rs | 1 -
 src/main.rs    | 3 +--
 3 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/Cargo.toml b/Cargo.toml
index 6050342..8a1ee83 100644
--- 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
index 6fe7b10..ffa538b 100644
--- 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
index 6a8810a..bc30cc2 100644
--- 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,
     },