From 2f51597633c5287c863605c44ce5b1eaeee2b79b Mon Sep 17 00:00:00 2001
From: Jean Pierre ELBERS <jeanpierre.elbers@ist.ac.at>
Date: Tue, 15 Feb 2022 12:16:32 +0100
Subject: [PATCH] changed GzDecoder to MultiGzDecoder

---
 .gitignore                 | 10 ++++++++++
 Cargo.toml                 |  2 +-
 src/bin/utils/build_sdb.rs |  4 ++--
 src/bin/utils/seqmap.rs    |  4 ++--
 4 files changed, 15 insertions(+), 5 deletions(-)
 create mode 100644 .gitignore

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..0aba1a3
--- /dev/null
+++ b/.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
diff --git a/Cargo.toml b/Cargo.toml
index 4faf5e6..7fb6ef3 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "peregrine-r"
-version = "0.4.12"
+version = "0.4.13"
 authors = ["Jason Chin <cschin@omnibio.ai>"]
 edition = "2018"
 build = "build.rs"
diff --git a/src/bin/utils/build_sdb.rs b/src/bin/utils/build_sdb.rs
index 4b9e646..a663ea6 100644
--- a/src/bin/utils/build_sdb.rs
+++ b/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();
diff --git a/src/bin/utils/seqmap.rs b/src/bin/utils/seqmap.rs
index 186416c..aa284e1 100644
--- a/src/bin/utils/seqmap.rs
+++ b/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() {