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Fix bug with reverse complement not being normalized. #65

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Fix bug with reverse complement not being normalized. #65

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2 changes: 1 addition & 1 deletion Cargo.lock
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8 changes: 4 additions & 4 deletions lib/src/sketch_schemes/mash.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -67,10 +67,10 @@ impl MashSketcher {

impl SketchScheme for MashSketcher {
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
seq.normalize(false).canonical_kmers(self.kmer_length, &rc)
let norm_seq = seq.normalize(false);
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I think in practice this trait is not well thought. The process function should take a &Sequence since we do not need anything from the &SequenceRecord and normalizing it here implicitly would allocate twice for normalized sequence if you need that elsewhere. In that case you would still need to call normalize before calling process though.

self.total_bases += norm_seq.sequence().len() as u64;
let rc = norm_seq.reverse_complement();
for (_, kmer, is_rev_complement) in norm_seq.canonical_kmers(self.kmer_length, &rc)
{
let rc_count = u8::from(is_rev_complement);
self.push(kmer, rc_count);
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8 changes: 4 additions & 4 deletions lib/src/sketch_schemes/scaled.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -65,10 +65,10 @@ impl ScaledSketcher {

impl SketchScheme for ScaledSketcher {
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
seq.normalize(false).canonical_kmers(self.kmer_length, &rc)
let norm_seq = seq.normalize(false);
self.total_bases += norm_seq.sequence().len() as u64;
let rc = norm_seq.reverse_complement();
for (_, kmer, is_rev_complement) in norm_seq.canonical_kmers(self.kmer_length, &rc)
{
let rc_count = u8::from(is_rev_complement);
self.push(kmer, rc_count);
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