Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int…

…o add/zipfile_use_storage
sourmash-bio · Jun 25, 2021 · fc0c6fe · fc0c6fe
2 parents 65646fb + a5a52b1
commit fc0c6fe
Show file tree

Hide file tree

Showing 9 changed files with 32 additions and 32 deletions.
diff --git a/src/core/src/cmd.rs b/src/core/src/cmd.rs
@@ -24,7 +24,7 @@ pub fn prepare(index_path: &str) -> Result<(), Error> {
 
 impl Signature {
     pub fn from_params(params: &ComputeParameters) -> Signature {
-        let template = build_template(&params);
+        let template = build_template(params);
 
         Signature::builder()
             .hash_function("0.murmur64")

diff --git a/src/core/src/index/mod.rs b/src/core/src/index/mod.rs
@@ -114,11 +114,11 @@ where
     N: Comparable<L>,
 {
     fn similarity(&self, other: &L) -> f64 {
-        (*self).similarity(&other)
+        (*self).similarity(other)
     }
 
     fn containment(&self, other: &L) -> f64 {
-        (*self).containment(&other)
+        (*self).containment(other)
     }
 }
 
@@ -195,7 +195,7 @@ impl SigStore<Signature> {
         // TODO: better matching here, what if it is not a mh?
         if let Sketch::MinHash(mh) = &ng.signatures[0] {
             if let Sketch::MinHash(omh) = &ong.signatures[0] {
-                return mh.count_common(&omh, false).unwrap() as u64;
+                return mh.count_common(omh, false).unwrap() as u64;
             }
         }
         unimplemented!();
@@ -252,7 +252,7 @@ impl Comparable<SigStore<Signature>> for SigStore<Signature> {
         // TODO: better matching here, what if it is not a mh?
         if let Sketch::MinHash(mh) = &ng.signatures[0] {
             if let Sketch::MinHash(omh) = &ong.signatures[0] {
-                return mh.similarity(&omh, true, false).unwrap();
+                return mh.similarity(omh, true, false).unwrap();
             }
         }
 
@@ -275,7 +275,7 @@ impl Comparable<SigStore<Signature>> for SigStore<Signature> {
         // TODO: better matching here, what if it is not a mh?
         if let Sketch::MinHash(mh) = &ng.signatures[0] {
             if let Sketch::MinHash(omh) = &ong.signatures[0] {
-                let common = mh.count_common(&omh, false).unwrap();
+                let common = mh.count_common(omh, false).unwrap();
                 let size = mh.size();
                 return common as f64 / size as f64;
             }
@@ -290,7 +290,7 @@ impl Comparable<Signature> for Signature {
         // TODO: better matching here, what if it is not a mh?
         if let Sketch::MinHash(mh) = &self.signatures[0] {
             if let Sketch::MinHash(omh) = &other.signatures[0] {
-                return mh.similarity(&omh, true, false).unwrap();
+                return mh.similarity(omh, true, false).unwrap();
             }
         }
 
@@ -310,7 +310,7 @@ impl Comparable<Signature> for Signature {
         // TODO: better matching here, what if it is not a mh?
         if let Sketch::MinHash(mh) = &self.signatures[0] {
             if let Sketch::MinHash(omh) = &other.signatures[0] {
-                let common = mh.count_common(&omh, false).unwrap();
+                let common = mh.count_common(omh, false).unwrap();
                 let size = mh.size();
                 return common as f64 / size as f64;
             }

diff --git a/src/core/src/index/sbt/mhbt.rs b/src/core/src/index/sbt/mhbt.rs
@@ -76,13 +76,13 @@ impl Comparable<Node<Nodegraph>> for Node<Nodegraph> {
     fn similarity(&self, other: &Node<Nodegraph>) -> f64 {
         let ng: &Nodegraph = self.data().unwrap();
         let ong: &Nodegraph = other.data().unwrap();
-        ng.similarity(&ong)
+        ng.similarity(ong)
     }
 
     fn containment(&self, other: &Node<Nodegraph>) -> f64 {
         let ng: &Nodegraph = self.data().unwrap();
         let ong: &Nodegraph = other.data().unwrap();
-        ng.containment(&ong)
+        ng.containment(ong)
     }
 }
 

diff --git a/src/core/src/index/sbt/mod.rs b/src/core/src/index/sbt/mod.rs
@@ -822,7 +822,7 @@ impl BinaryTree {
                 let mut similar_node_pos = 0;
                 let mut current_max = 0;
                 for (pos, cmpe) in current_round.iter().enumerate() {
-                    let common = BinaryTree::intersection_size(&next_node, &cmpe);
+                    let common = BinaryTree::intersection_size(&next_node, cmpe);
                     if common > current_max {
                         current_max = common;
                         similar_node_pos = pos;

diff --git a/src/core/src/signature.rs b/src/core/src/signature.rs
@@ -134,7 +134,7 @@ pub trait SigsTrait {
 
         if hash_function.protein() {
             for aa_kmer in seq.windows(ksize) {
-                let hash = crate::_hash_murmur(&aa_kmer, self.seed());
+                let hash = crate::_hash_murmur(aa_kmer, self.seed());
                 self.add_hash(hash);
             }
             return Ok(());
@@ -151,7 +151,7 @@ pub trait SigsTrait {
         };
 
         for aa_kmer in aa_seq.windows(ksize) {
-            let hash = crate::_hash_murmur(&aa_kmer, self.seed());
+            let hash = crate::_hash_murmur(aa_kmer, self.seed());
             self.add_hash(hash);
         }
 
@@ -478,7 +478,7 @@ impl Signature {
             self.signatures
                 .iter_mut()
                 .for_each(|sketch| {
-                    sketch.add_sequence(&seq, force).unwrap(); }
+                    sketch.add_sequence(seq, force).unwrap(); }
                 );
         }
         }
@@ -498,7 +498,7 @@ impl Signature {
             self.signatures
                 .iter_mut()
                 .try_for_each(|sketch| {
-                    sketch.add_protein(&seq) }
+                    sketch.add_protein(seq) }
                 )?;
         }
         }

diff --git a/src/core/src/sketch/hyperloglog/estimators.rs b/src/core/src/sketch/hyperloglog/estimators.rs
@@ -120,7 +120,7 @@ pub fn joint_mle(
     let mut ceq = vec![0; q + 2];
 
     for (k1_, k2_) in k1.iter().zip(k2.iter()) {
-        match k1_.cmp(&k2_) {
+        match k1_.cmp(k2_) {
             cmp::Ordering::Less => {
                 c1[*k1_ as usize] += 1;
                 cg2[*k2_ as usize] += 1;

diff --git a/src/core/src/sketch/hyperloglog/mod.rs b/src/core/src/sketch/hyperloglog/mod.rs
@@ -120,7 +120,7 @@ impl HyperLogLog {
         wtr.write_u8(self.p as u8)?; // number of bits used for indexing
         wtr.write_u8(self.q as u8)?; // number of bits used for counting leading zeroes
         wtr.write_u8(self.ksize as u8)?; // ksize
-        wtr.write_all(&self.registers.as_slice())?;
+        wtr.write_all(self.registers.as_slice())?;
 
         Ok(())
     }

diff --git a/src/core/src/sketch/minhash.rs b/src/core/src/sketch/minhash.rs
@@ -597,8 +597,8 @@ impl KmerMinHash {
                 self.num,
             );
 
-            combined_mh.merge(&self)?;
-            combined_mh.merge(&other)?;
+            combined_mh.merge(self)?;
+            combined_mh.merge(other)?;
 
             let it1 = Intersection::new(self.mins.iter(), other.mins.iter());
 
@@ -630,8 +630,8 @@ impl KmerMinHash {
                 self.num,
             );
 
-            combined_mh.merge(&self)?;
-            combined_mh.merge(&other)?;
+            combined_mh.merge(self)?;
+            combined_mh.merge(other)?;
 
             let it1 = Intersection::new(self.mins.iter(), other.mins.iter());
 
@@ -721,9 +721,9 @@ impl KmerMinHash {
             let downsampled_mh = second.downsample_max_hash(first.max_hash)?;
             first.similarity(&downsampled_mh, ignore_abundance, false)
         } else if ignore_abundance || self.abunds.is_none() || other.abunds.is_none() {
-            self.jaccard(&other)
+            self.jaccard(other)
         } else {
-            self.angular_similarity(&other)
+            self.angular_similarity(other)
         }
     }
 
@@ -1311,7 +1311,7 @@ impl KmerMinHashBTree {
 
                 for hash in &self.mins {
                     *new_abunds.entry(*hash).or_insert(0) +=
-                        abunds.get(&hash).unwrap_or(&0) + oabunds.get(&hash).unwrap_or(&0);
+                        abunds.get(hash).unwrap_or(&0) + oabunds.get(hash).unwrap_or(&0);
                 }
                 self.abunds = Some(new_abunds)
             }
@@ -1378,8 +1378,8 @@ impl KmerMinHashBTree {
                 self.num,
             );
 
-            combined_mh.merge(&self)?;
-            combined_mh.merge(&other)?;
+            combined_mh.merge(self)?;
+            combined_mh.merge(other)?;
 
             let it1 = Intersection::new(self.mins.iter(), other.mins.iter());
 
@@ -1410,8 +1410,8 @@ impl KmerMinHashBTree {
                 self.num,
             );
 
-            combined_mh.merge(&self)?;
-            combined_mh.merge(&other)?;
+            combined_mh.merge(self)?;
+            combined_mh.merge(other)?;
 
             let it1 = Intersection::new(self.mins.iter(), other.mins.iter());
 
@@ -1455,7 +1455,7 @@ impl KmerMinHashBTree {
         let b_sq: u64 = other_abunds.values().map(|a| (a * a)).sum();
 
         for (hash, value) in abunds.iter() {
-            if let Some(oa) = other_abunds.get(&hash) {
+            if let Some(oa) = other_abunds.get(hash) {
                 prod += value * oa
             }
         }
@@ -1486,9 +1486,9 @@ impl KmerMinHashBTree {
             let downsampled_mh = second.downsample_max_hash(first.max_hash)?;
             first.similarity(&downsampled_mh, ignore_abundance, false)
         } else if ignore_abundance || self.abunds.is_none() || other.abunds.is_none() {
-            self.jaccard(&other)
+            self.jaccard(other)
         } else {
-            self.angular_similarity(&other)
+            self.angular_similarity(other)
         }
     }
 

diff --git a/src/core/src/sketch/nodegraph.rs b/src/core/src/sketch/nodegraph.rs
@@ -202,7 +202,7 @@ impl Nodegraph {
                 let len = size_of::<u32>() * slice.len();
                 slice::from_raw_parts(slice.as_ptr() as *const u8, len)
             };
-            wtr.write_all(&buf)?;
+            wtr.write_all(buf)?;
             // Replace when byteorder PR is released
 
             if rem != 0 {