Fix major bug in write_ben_file function

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "binary-ensemble"
-version = "0.1.1"
+version = "0.1.2"
 edition = "2021"
 authors = ["Peter Rock <[email protected]>"]
 exclude = ["example/"]

TODO.md

@@ -16,3 +16,12 @@
 - [ ] Make a special MCMC writer for ben that add a self-loop counter to the start of 
   the next item. This will be really useful for reducing the size of any chain that
   has a high rejection ratio (e.g. reversible)
+
+- [ ] Add an overwrite option to `reben` rather than just doing it by default
+
+- [ ] Change the `-s` flag in the "shapefile" parameter in `reben` to a `-d`
+
+- [ ] Add a reverse mode to reben to make reverting the labeling a little bit
+  easier for the end user
+
+- [ ] Add a `jsonl` mode to reben to relabel the `jsonl` file.

src/bin/ben.rs

@@ -25,7 +25,7 @@ enum Mode {
 #[command(
     name = "Binary Ensamble CLI Tool",
     about = "This is a command line tool for encoding and decoding binary ensamble files.",
-    version = "0.1.1"
+    version = "0.1.2"
 )]
 struct Args {
     /// Mode to run the program in (encode, decode, or read).

src/bin/reben.rs

@@ -24,8 +24,10 @@ enum Mode {
         "This is a command line tool for relabeling binary ensambles ",
         "to help improve compression ratios for BEN and XBEN files."
     ),
-    version = "0.1.1"
+    version = "0.1.2"
 )]
+
+// TODO: Change the name of shape_file to dual_graph_file.
 struct Args {
     /// Input file to read from.
     #[arg()]
@@ -66,6 +68,7 @@ fn main() {
 
     match &args.mode {
         Mode::Json => {
+            // TODO: Change the input file here to the shape file.
             let input_file = File::open(&args.input_file).expect("Could not open input file.");
             let reader = BufReader::new(input_file);
 

src/encode/mod.rs

@@ -25,7 +25,7 @@ pub mod translate;
 
 use crate::utils::*;
 use serde_json::Value;
-use std::io::{self, BufRead, Cursor, Result, Write};
+use std::io::{self, BufRead, Cursor, Read, Result, Write};
 use xz2::write::XzEncoder;
 
 use self::translate::ben_to_ben32_lines;
@@ -117,7 +117,7 @@ impl<W: Write> XBenEncoder<W> {
         // Create a new reader that prepends buff back onto the original reader
         let mut reader = if buff != b"STANDARD BEN FILE".as_slice() {
             let cursor = Cursor::new(buff.to_vec());
-            let reader = reader.chain(cursor);
+            let reader = cursor.chain(reader);
             Box::new(reader) as Box<dyn BufRead>
         } else {
             Box::new(reader)