Break public API, simplify key mgmt and tests

Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "crypt4gh"
 version = "0.4.1"
-authors = ["Roberto <roberto.ariosa@crg.eu>"]
+authors = ["Roberto <roberto.ariosa@crg.eu>", "Marko Malenic <marko.malenic@umccr.org>", "Roman Valls Guimera <brainstorm@nopcode.org>"]
 edition = "2021"
 license = "Apache-2.0"
 description = "Encryption and decryption implementation of the Crypt4GH encryption format."
@@ -23,10 +23,10 @@ path = "src/bin.rs"
 clap = { version = "4", features = ["derive", "env"] }
 regex = "1.5"
 rpassword = "7"
-base64 = "0.21"
+base64 = "0.22"
 lazy_static = "1.4"
 chacha20poly1305 = "0.10"
-crypto_kx = { version = "0.2.1" }
+crypto_kx = { version = "0.2" }
 scrypt = { version = "0.11" }
 bcrypt-pbkdf = { version = "0.10" }
 aes = { version = "0.8" }
@@ -38,15 +38,26 @@ serde = { version = "1", features = ["derive"] }
 log = "0.4"
 pretty_env_logger = "0.5"
 thiserror = "1"
-itertools = "0.11"
+itertools = "0.13"
 rand = "0.8"
 rand_chacha = "0.3"
 ed25519_to_curve25519 = "0.2"
 
-curve25519-dalek = "4.0.0"
+curve25519-dalek = "4"
+ssh-key = { version = "0.6.4", features = ["ed25519"] }
+bytes = "1.5.0"
+rustls = "0.23"
+tokio = { version = "1", features = [ "io-util", "test-util", "macros", "rt-multi-thread" ] }
+futures = "0.3"
+pin-project-lite = "0.2.13"
+tokio-util = { version = "0.7", features = ["codec"] }
+futures-util = "0.3.30"
 
 [dev-dependencies]
-testresult = "0.3"
+testresult = "0.4"
+noodles-bam = "0.65"
+noodles-sam = "0.62"
+noodles = { version = "0.78", features = [ "sam", "bam", "async" ] }
 
 [profile.release]
 lto = true

README.md

@@ -89,16 +89,12 @@ Use the exposed functions:
 ```rust
 pub fn encrypt<R: Read, W: Write>(
     recipient_keys: &HashSet<Keys>,
-    read_buffer: &mut R,
-    write_buffer: &mut W,
     range_start: usize,
     range_span: Option<usize>
 ) -> Result<()>
 
 pub fn decrypt<R: Read, W: Write>(
     keys: Vec<Keys>,
-    read_buffer: &mut R,
-    write_buffer: &mut W,
     range_start: usize,
     range_span: Option<usize>,
     sender_pubkey: Option<Vec<u8>>,
@@ -107,15 +103,11 @@ pub fn decrypt<R: Read, W: Write>(
 pub fn reencrypt<R: Read, W: Write>(
     keys: Vec<Keys>,
     recipient_keys: HashSet<Keys>,
-    read_buffer: &mut R,
-    write_buffer: &mut W,
     trim: bool,
 ) -> Result<()>
 
 pub fn rearrange<R: Read, W: Write>(
     keys: Vec<Keys>,
-    read_buffer: &mut R,
-    write_buffer: &mut W,
     range_start: usize,
     range_span: Option<usize>,
 ) -> Result<()>