From 17cb9856dc46f29e7af63b6ec7de342313be0ff8 Mon Sep 17 00:00:00 2001
From: Rory Coffey <coffeyrt@gmail.com>
Date: Tue, 26 Sep 2023 13:20:54 -0400
Subject: [PATCH] moved back to flate2 using multigzDecoder for blocked gzip
 files

---
 Cargo.toml   | 4 ++--
 src/input.rs | 7 +++----
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/Cargo.toml b/Cargo.toml
index 055b129..48f79c9 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,7 +1,7 @@
 [package]
 name = "barcode-count"
 description = "NGS barcode counter for DEL, CRISPR-seq, and Barcode-seq"
-version = "0.11.0"
+version = "0.11.1"
 edition = "2021"
 license = "Apache-2.0"
 readme = "README.md"
@@ -25,4 +25,4 @@ itertools = "0.10"
 num_cpus = "1.0"
 chrono = "0.4"
 num-format = "0.4"
-rust-htslib = "0.44"
+flate2= "1.0"
diff --git a/src/input.rs b/src/input.rs
index 45dbb62..06d9937 100644
--- a/src/input.rs
+++ b/src/input.rs
@@ -10,7 +10,7 @@ use std::{
         Arc, Mutex,
     },
 };
-use rust_htslib::bgzf;
+use flate2::read::MultiGzDecoder;
 
 use crate::parse::RawSequenceRead;
 
@@ -30,10 +30,9 @@ pub fn read_fastq(
 
     // Create a fastq line reader which keeps track of line number, reads, and posts the sequence to the shared vector
     let mut fastq_line_reader = FastqLineReader::new(seq_clone, exit_clone);
-
+    let fastq_file = File::open(&fastq).context(format!("Failed to open file: {}", fastq))?; // open file
     // If the file is not gzipped use BufReader to read in lines
     if !fastq.ends_with("fastq.gz") {
-        let fastq_file = File::open(&fastq).context(format!("Failed to open file: {}", fastq))?; // open file
         // If the file does not end with fastq, return with an error
         if !fastq.ends_with("fastq") {
             bail!("This program only works with *.fastq files and *.fastq.gz files.  The latter is still experimental")
@@ -61,7 +60,7 @@ pub fn read_fastq(
         println!("If this program stops reading before the expected number of sequencing reads, unzip the gzipped fastq and rerun.");
         println!();
         // stream in first by decoding with GzDecoder, the reading into buffer
-        let mut reader = BufReader::new(bgzf::Reader::from_path(fastq)?);
+        let mut reader = BufReader::new(MultiGzDecoder::new(fastq_file));
 
         let mut stdout = std::io::stdout();
         let mut lock = stdout.lock();