Borrow sequence records (#61)

onecodex · Dec 13, 2022 · a316f29 · a316f29
1 parent d0475df
commit a316f29
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Showing 7 changed files with 7 additions and 7 deletions.
diff --git a/cli/Cargo.toml b/cli/Cargo.toml
@@ -16,7 +16,7 @@ path = "src/main.rs"
 
 [dependencies]
 clap = "2.33.0"
-finch = { version = "0.4", path = "../lib" }
+finch = { version = "0.5", path = "../lib" }
 serde_json = "1"
 anyhow = "1"
 

diff --git a/lib/Cargo.toml b/lib/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "finch"
-version = "0.4.3"
+version = "0.5.0"
 authors = ["One Codex <[email protected]>"]
 description = "An implementation of min-wise independent permutation locality sensitive hashing ('MinHashing') for genomic data and command-line utility for manipulation."
 keywords = ["minhash", "bioinformatics", "sketches"]

diff --git a/lib/src/lib.rs b/lib/src/lib.rs
@@ -64,7 +64,7 @@ pub fn sketch_stream<'a>(
         if seq_type.is_none() {
             seq_type = Some(seqrec.format());
         }
-        sketcher.process(seqrec);
+        sketcher.process(&seqrec);
     }
 
     // disable filtering for FASTA files unless it was explicitly specified

diff --git a/lib/src/sketch_schemes/counts.rs b/lib/src/sketch_schemes/counts.rs
@@ -23,7 +23,7 @@ impl AllCountsSketcher {
 }
 
 impl SketchScheme for AllCountsSketcher {
-    fn process(&mut self, seq: SequenceRecord) {
+    fn process(&mut self, seq: &SequenceRecord) {
         for (_, kmer, _) in seq.normalize(false).bit_kmers(self.k, false) {
             self.counts[kmer.0 as usize] = self.counts[kmer.0 as usize].saturating_add(1);
         }

diff --git a/lib/src/sketch_schemes/mash.rs b/lib/src/sketch_schemes/mash.rs
@@ -66,7 +66,7 @@ impl MashSketcher {
 }
 
 impl SketchScheme for MashSketcher {
-    fn process(&mut self, seq: SequenceRecord) {
+    fn process(&mut self, seq: &SequenceRecord) {
         self.total_bases += seq.sequence().len() as u64;
         let rc = seq.reverse_complement();
         for (_, kmer, is_rev_complement) in

diff --git a/lib/src/sketch_schemes/mod.rs b/lib/src/sketch_schemes/mod.rs
@@ -22,7 +22,7 @@ pub struct KmerCount {
 }
 
 pub trait SketchScheme {
-    fn process(&mut self, seq: SequenceRecord);
+    fn process(&mut self, seq: &SequenceRecord);
     fn total_bases_and_kmers(&self) -> (u64, u64);
     fn to_vec(&self) -> Vec<KmerCount>;
     fn parameters(&self) -> SketchParams;

diff --git a/lib/src/sketch_schemes/scaled.rs b/lib/src/sketch_schemes/scaled.rs
@@ -65,7 +65,7 @@ impl ScaledSketcher {
 }
 
 impl SketchScheme for ScaledSketcher {
-    fn process(&mut self, seq: SequenceRecord) {
+    fn process(&mut self, seq: &SequenceRecord) {
         self.total_bases += seq.sequence().len() as u64;
         let rc = seq.reverse_complement();
         for (_, kmer, is_rev_complement) in