Merge pull request #3 from jelber2/main

(1) changed `GzDecoder` to `MultiGzDecoder`
(2) add `.gitignore`
(3) bump version to 0.4.13

.gitignore

@@ -0,0 +1,10 @@
+# Generated by Cargo
+# will have compiled files and executables
+/target/
+/target
+# Remove Cargo.lock from gitignore if creating an executable, leave it for libraries
+# More information here https://doc.rust-lang.org/cargo/guide/cargo-toml-vs-cargo-lock.html
+Cargo.lock
+
+# These are backup files generated by rustfmt
+**/*.rs.bk

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "peregrine-r"
-version = "0.4.12"
+version = "0.4.13"
 authors = ["Jason Chin <[email protected]>"]
 edition = "2018"
 build = "build.rs"

src/bin/utils/build_sdb.rs

@@ -9,7 +9,7 @@
 
 #![allow(dead_code)]
 
-use flate2::bufread::GzDecoder;
+use flate2::bufread::MultiGzDecoder;
 use rayon::prelude::*;
 use std::fs::File;
 use std::io::prelude::*;
@@ -273,7 +273,7 @@ pub fn build(seq_list_file: &String, out_prefix: &String) -> Result<usize, io::E
         let _ = reader.seek(SeekFrom::Start(0));
         let mut seqs = Vec::<(u32, Vec<u8>, Vec<u8>)>::new();
         if is_gzfile {
-            let fastx_buf = BufReader::new(GzDecoder::new(&mut reader));
+            let fastx_buf = BufReader::new(MultiGzDecoder::new(&mut reader));
             let mut fastx_reader = FastxReader::new(fastx_buf, &input_fn)?;
             while let Some(r) = fastx_reader.next_rec() {
                 let r = r.unwrap();

src/bin/utils/seqmap.rs

@@ -26,7 +26,7 @@ use std::io::{BufRead, BufReader, BufWriter, Read, Seek, SeekFrom, Write};
 pub type MapIntervalRecord = [u32; 8];
 pub type MapIntervals = FxHashMap<u32, IntervalTree<u32, MapIntervalRecord>>;
 pub type Shmmrs = Vec<Vec<MM128>>;
-use flate2::bufread::GzDecoder;
+use flate2::bufread::MultiGzDecoder;
 use petgraph::graphmap::DiGraphMap;
 use petgraph::unionfind::UnionFind;
 use rayon::prelude::*;
@@ -89,7 +89,7 @@ impl SeqDB {
 
         reader.seek(SeekFrom::Start(0))?;
         if is_gzfile {
-            let fastx_buf = BufReader::new(GzDecoder::new(&mut reader));
+            let fastx_buf = BufReader::new(MultiGzDecoder::new(&mut reader));
             let mut fastx_reader = FastxReader::new(fastx_buf, &self.filepath)?;
             let mut sid = 0;
             while let Some(rec) = fastx_reader.next_rec() {