diff --git a/Cargo.toml b/Cargo.toml
index 3646fd7c..34b680e1 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -19,9 +19,7 @@ path = "src/main.rs"
 [dependencies]
 anstyle = "1.0.0"
 anyhow = "1.0.58"
-bamlift = {path = "bamlift", version = "0.3"}
 bio = "1.2.0"
-bio-io = {path = "bio-io", version = "^0.3.2" }
 clap = {version = "4.4.6", features = ["cargo", "string", "wrap_help", "color", "unstable-styles", "derive"], optional = true}
 clap_complete = {version = "4.0.6", optional = true}
 clap_mangen = {version = "0.2.5", optional = true}
diff --git a/bamlift/src/lib.rs b/src/bamlift/mod.rs
similarity index 100%
rename from bamlift/src/lib.rs
rename to src/bamlift/mod.rs
diff --git a/bio-io/src/lib.rs b/src/bio_io/mod.rs
similarity index 100%
rename from bio-io/src/lib.rs
rename to src/bio_io/mod.rs
diff --git a/src/lib.rs b/src/lib.rs
index e0478a54..2700f65e 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -26,6 +26,10 @@ pub mod decorator;
 
 pub mod footprint;
 
+pub mod bamlift;
+
+pub mod bio_io;
+
 use anyhow::Result;
 use bio_io::*;
 #[cfg(feature = "predict")]