Unify FASTX parsing functions & allow streaming gz/bz/etc

Cargo.toml

@@ -12,18 +12,18 @@ edition = "2018"
 
 [features]
 default = ["compression"]
-compression = ["bzip2", "flate2", "xz2", "zip"]
+compression = ["bzip2", "flate2", "xz2"]
 
 [dependencies]
 flate2 = { version="1.0.6", optional=true }
 bzip2 = { version="0.3.3", optional=true }
 xz2 = { version="0.1.6", optional=true }
-zip = { version="0.5.0", optional=true }
 memchr = "2.2.0"
 
 [dev-dependencies]
 bencher = "0.1.5"
 
 [[bench]]
+path = "tests/benchmark.rs"
 name = "benchmark"
 harness = false

src/bitkmer.rs

@@ -223,8 +223,8 @@ pub fn bitmer_to_bytes(kmer: BitKmer) -> Vec<u8> {
     // math to figure out where they start (this helps us just pop the bases on the end
     // of the working buffer as we read them off "left to right")
     let offset = (kmer.1 - 1) * 2;
-    let bitmask =
-        BitKmerSeq::pow(2, u32::from(2 * kmer.1 - 1)) + BitKmerSeq::pow(2, u32::from(2 * kmer.1 - 2));
+    let bitmask = BitKmerSeq::pow(2, u32::from(2 * kmer.1 - 1))
+        + BitKmerSeq::pow(2, u32::from(2 * kmer.1 - 2));
 
     for _ in 0..kmer.1 {
         let new_char = (new_kmer & bitmask) >> offset;

src/buffer.rs

@@ -4,7 +4,7 @@ use std::marker::PhantomData;
 use crate::util::ParseError;
 
 pub struct RecReader<'a> {
-    file: &'a mut io::Read,
+    file: &'a mut dyn io::Read,
     last: bool,
     pub buf: Vec<u8>,
 }
@@ -20,7 +20,7 @@ impl<'a> RecReader<'a> {
     /// Under some very rare circumstances (setting a `buf_size` larger than 2 Gb
     /// on Mac OS X) a panic can occur. Please use a smaller buffer in this case.
     pub fn new(
-        file: &'a mut io::Read,
+        file: &'a mut dyn io::Read,
         buf_size: usize,
         header: &[u8],
     ) -> Result<RecReader<'a>, ParseError> {