Switch to using compress_io from crates.io

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "ont_demult"
-version = "0.3.2"
+version = "0.3.3"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
@@ -11,4 +11,4 @@ log = "~0.4"
 stderrlog = "~0.5"
 clap = {version = "~3.1", features = ["cargo"]}
 anyhow = "~1.0"
-compress_io = { git = "https://github.com/heathsc/compress_io.git" }
+compress_io = "~0.4"

README.md

@@ -216,6 +216,7 @@ as a cut site name, or it will cause the files to be overwritten!
 
 ## Changes
 
+- 0.3.3 Switch to using compress_io from crates.io
 - 0.3.2 Fix bug in Xor selection mode where a read only matching the end site would not be selected
 - 0.3.1 Correct headers in results file.  Clean up output.
 - 0.3.1 Fix compress option which was not being read correctly.

src/fastq.rs

@@ -5,7 +5,7 @@ use std::{
     path::Path,
 };
 
-use compress_io::compress::CompressIo;
+use compress_io::compress::{CompressIo, Writer};
 
 fn gen_err(s: &str, line: usize) -> io::Error {
     Error::new(ErrorKind::Other, format!("{} at line {}", s, line))
@@ -91,7 +91,7 @@ impl FastqFile {
         self.buf[1].trim().len()
     }
 
-    pub fn write_rec(&self, wrt: &mut BufWriter<Box<dyn Write>>) -> io::Result<()> {
+    pub fn write_rec(&self, wrt: &mut BufWriter<Writer>) -> io::Result<()> {
         write!(wrt, "{}{}+\n{}", self.buf[0], self.buf[1], self.buf[2])
     }
 }

src/output.rs

@@ -1,14 +1,14 @@
 use std::collections::HashMap;
-use std::io::{self, Write, BufWriter};
+use std::io::{self, BufWriter};
 
 use compress_io::{
-    compress::CompressIo,
+    compress::{CompressIo, Writer},
     compress_type::CompressType
 };
 
 use crate::params::Param;
 
-pub fn open_output_file<S: AsRef<str>>(name: S, param: &Param) -> io::Result<BufWriter<Box<dyn Write>>> {
+pub fn open_output_file<S: AsRef<str>>(name: S, param: &Param) -> io::Result<BufWriter<Writer>> {
     let fname = format!("{}_{}", param.prefix(), name.as_ref());
     let mut c = CompressIo::new();
     if param.compress() {
@@ -18,10 +18,10 @@ pub fn open_output_file<S: AsRef<str>>(name: S, param: &Param) -> io::Result<Buf
 }
 
 pub struct OutputFiles<'a> {
-    pub unmapped: Option<BufWriter<Box<dyn Write>>>,
-    pub low_mapq: Option<BufWriter<Box<dyn Write>>>,
-    pub unmatched: Option<BufWriter<Box<dyn Write>>>,
-    pub site_hash: HashMap<&'a str, BufWriter<Box<dyn Write>>>,
+    pub unmapped: Option<BufWriter<Writer>>,
+    pub low_mapq: Option<BufWriter<Writer>>,
+    pub unmatched: Option<BufWriter<Writer>>,
+    pub site_hash: HashMap<&'a str, BufWriter<Writer>>,
 }
 
 impl<'a> OutputFiles<'a> {