From e03d2e9761eecab4d40024d90cc12b3e158ffefe Mon Sep 17 00:00:00 2001
From: Luiz Irber <luiz.irber@gmail.com>
Date: Wed, 8 Jul 2020 09:00:49 -0700
Subject: [PATCH] bump needletail

---
 src/core/Cargo.toml              |  4 ++--
 src/core/src/index/linear.rs     |  2 +-
 src/core/src/index/sbt/mod.rs    |  2 +-
 src/core/src/signature.rs        | 19 ++++++++-----------
 src/core/src/sketch/nodegraph.rs |  2 +-
 5 files changed, 13 insertions(+), 16 deletions(-)

diff --git a/src/core/Cargo.toml b/src/core/Cargo.toml
index 1ef2a83256..4b1f084b74 100644
--- a/src/core/Cargo.toml
+++ b/src/core/Cargo.toml
@@ -31,7 +31,7 @@ fixedbitset = "0.3.0"
 log = "0.4.8"
 md5 = "0.7.0"
 murmurhash3 = "0.0.5"
-niffler = { version = "3.0.0", default-features = false, features = [ "gz" ], git = "https://github.com/luizirber/niffler.git", branch = "send" }
+niffler = { version = "2.2.0", default-features = false, features = [ "gz" ] }
 nohash-hasher = "0.2.0"
 once_cell = "1.3.1"
 rayon = { version = "1.3.0", optional = true }
@@ -61,7 +61,7 @@ rand = "0.7.3"
 tempfile = "3.1.0"
 
 [dev-dependencies.needletail]
-version = "0.3.2"
+version = "0.4.0"
 default-features = false
 
 [[bench]]
diff --git a/src/core/src/index/linear.rs b/src/core/src/index/linear.rs
index 0cc627f185..009ebbaadc 100644
--- a/src/core/src/index/linear.rs
+++ b/src/core/src/index/linear.rs
@@ -153,7 +153,7 @@ where
 
     pub fn from_reader<R, P>(rdr: R, path: P) -> Result<LinearIndex<L>, Error>
     where
-        R: Read + Send,
+        R: Read,
         P: AsRef<Path>,
     {
         // TODO: check https://serde.rs/enum-representations.html for a
diff --git a/src/core/src/index/sbt/mod.rs b/src/core/src/index/sbt/mod.rs
index dc8f13d17b..d8e3d2c240 100644
--- a/src/core/src/index/sbt/mod.rs
+++ b/src/core/src/index/sbt/mod.rs
@@ -137,7 +137,7 @@ where
 
     pub fn from_reader<R, P>(mut rdr: R, path: P) -> Result<SBT<Node<U>, T>, Error>
     where
-        R: Read + Send,
+        R: Read,
         P: AsRef<Path>,
     {
         // TODO: I would love to do this, but I get an untagged enum error with
diff --git a/src/core/src/signature.rs b/src/core/src/signature.rs
index e9e5cab6c2..b8c7be11b2 100644
--- a/src/core/src/signature.rs
+++ b/src/core/src/signature.rs
@@ -229,7 +229,7 @@ impl Signature {
 
     pub fn from_reader<R>(rdr: R) -> Result<Vec<Signature>, Error>
     where
-        R: io::Read + Send,
+        R: io::Read,
     {
         let (rdr, _format) = niffler::get_reader(Box::new(rdr))?;
 
@@ -244,7 +244,7 @@ impl Signature {
         _scaled: Option<u64>,
     ) -> Result<Vec<Signature>, Error>
     where
-        R: io::Read + Send,
+        R: io::Read,
     {
         let orig_sigs = Signature::from_reader(buf)?;
 
@@ -426,7 +426,7 @@ mod test {
     use std::io::{BufReader, Read};
     use std::path::PathBuf;
 
-    use needletail::parse_sequence_reader;
+    use needletail::parse_fastx_reader;
 
     use crate::cmd::ComputeParameters;
     use crate::signature::SigsTrait;
@@ -559,14 +559,11 @@ mod test {
         let mut f = File::open("../../tests/test-data/ecoli.genes.fna").unwrap();
         let _ = f.read_to_end(&mut data);
 
-        parse_sequence_reader(
-            &data[..],
-            |_| {},
-            |rec| {
-                sig.add_sequence(&rec.seq, false).unwrap();
-            },
-        )
-        .unwrap();
+        let mut parser = parse_fastx_reader(&data[..]).unwrap();
+        while let Some(record) = parser.next() {
+            let record = record.unwrap();
+            sig.add_sequence(&record.seq(), false).unwrap();
+        }
 
         let sketches = sig.sketches();
         assert_eq!(sketches.len(), 12);
diff --git a/src/core/src/sketch/nodegraph.rs b/src/core/src/sketch/nodegraph.rs
index 059533de8a..34a34a8ca3 100644
--- a/src/core/src/sketch/nodegraph.rs
+++ b/src/core/src/sketch/nodegraph.rs
@@ -218,7 +218,7 @@ impl Nodegraph {
 
     pub fn from_reader<R>(rdr: R) -> Result<Nodegraph, Error>
     where
-        R: io::Read + Send,
+        R: io::Read,
     {
         let (mut rdr, _format) = niffler::get_reader(Box::new(rdr))?;