Updating gzp version to fix sstadick/gzp#31

.test/large.test.fa.gz.fai

@@ -0,0 +1,5 @@
+CEN1::Chr1:14841109-17559778	2718669	30	2718669	2718670
+CEN2::Chr2:3823791-6045243	2221452	2718728	2221452	2221453
+CEN3::Chr3:13597187-15733925	2136738	4940211	2136738	2136739
+CEN4::Chr4:4203901-6977949	2774048	7076978	2774048	2774049
+CEN5::Chr5:11784130-14551809	2767679	9851057	2767679	2767680

Cargo.toml

@@ -20,6 +20,10 @@ path = "src/main.rs"
 name = "rustybam"
 path = "src/main.rs"
 
+[[bin]]
+name = "test"
+path = "src/test.rs"
+
 [features]
 default = ["deflate_zlib_ng", "libdeflate"]
 deflate_rust = ["gzp/deflate_rust", "flate2/rust_backend"]
@@ -40,7 +44,7 @@ clap = {version = "3.0.0", features = ["yaml", "derive"]}
 colored = "2.0.0"
 env_logger = "0.9.0"
 flate2 = {version = "~1", default-features = false}
-gzp = {version = "0.9.2", default-features = false}
+gzp = {version = "0.9.3", default-features = false}
 itertools = "0.10.0"
 lazy_static = "1.4.0"
 log = "0.4.14"

src/fastx.rs

@@ -36,8 +36,8 @@ pub fn run_split_fastx(files: &[String], infile: &str) {
             out_idx = 0;
         }
     }
-
     // Close all the files.
+    // this breaks things?
     for mut out in outs {
         out.flush()
             .unwrap_or_else(|_| panic!("Error flushing output!"));

src/lib.rs

@@ -26,3 +26,5 @@ pub mod paf;
 pub mod suns;
 /// Functions for trimming query overlaps from a PAF file.
 pub mod trim_overlap;
+
+//pub mod test;

src/myio.rs

@@ -1,8 +1,8 @@
 use anyhow::Result;
 use flate2::read;
-use flate2::Compression;
 use gzp::deflate::Bgzf; //, Gzip, Mgzip, RawDeflate};
 use gzp::BgzfSyncReader;
+use gzp::Compression;
 use gzp::ZBuilder;
 use std::error::Error;
 use std::ffi::OsStr;
@@ -11,7 +11,7 @@ use std::io::{self, BufRead, BufReader, BufWriter, Write};
 use std::path::{Path, PathBuf};
 
 type DynResult<T> = Result<T, Box<dyn Error + 'static>>;
-const BUFFER_SIZE: usize = 128 * 1024;
+const BUFFER_SIZE: usize = 32 * 1024;
 
 /// Write normal or compressed files seamlessly
 /// Uses the presence of a `.gz` extension to decide
@@ -23,7 +23,7 @@ pub fn writer(filename: &str) -> Box<dyn Write> {
 
     if ext == Some(OsStr::new("gz")) {
         let writer = ZBuilder::<Bgzf, _>::new()
-            .num_threads(0) // must limit to 1 thread because if I don't I get an error when I write to multiple gzip files with large input strings
+            .num_threads(8)
             .compression_level(Compression::new(6))
             .from_writer(buffer);
         Box::new(writer)