Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

MRG: do a single pass reverse complement in kmers_and_hashes #82

Merged
merged 3 commits into from
Oct 28, 2024
Merged

MRG: do a single pass reverse complement in kmers_and_hashes #82

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
6fa36d2
compute revcomp once, not every time
ctb Oct 27, 2024
667610b
rm comment
ctb Oct 28, 2024
31a9a2a
run cargo fmt
Adamtaranto Oct 28, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
20 changes: 10 additions & 10 deletions src/lib.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -779,7 +779,7 @@ impl KmerCountTableIterator {

pub struct KmersAndHashesIter {
seq: String, // The sequence to iterate over
seqb: Vec<u8>, // Sequence bytes
seq_rc: String, // reverse complement sequence
ksize: usize, // K-mer size
pos: usize, // Current position in the sequence
end: usize, // The end position for k-mer extraction
Expand All @@ -791,8 +791,12 @@ impl KmersAndHashesIter {
pub fn new(seq: String, ksize: usize, skip_bad_kmers: bool) -> Self {
let seq = seq.to_ascii_uppercase(); // Ensure uppercase for uniformity
let seqb = seq.as_bytes().to_vec(); // Convert to bytes for hashing
let end = seq.len() - ksize + 1; // Calculate the endpoint for k-mer extraction
let seqb_rc = revcomp(&seqb);
let seq_rc = std::str::from_utf8(&seqb_rc)
.expect("invalid utf-8 sequence for rev comp")
.to_string();

let end = seq.len() - ksize + 1; // Calculate the endpoint for k-mer extraction
let hasher = SeqToHashes::new(
&seqb,
ksize.into(),
Expand All @@ -804,7 +808,7 @@ impl KmersAndHashesIter {

Self {
seq,
seqb,
seq_rc,
ksize,
pos: 0, // Start at the beginning of the sequence
end,
Expand All @@ -825,15 +829,11 @@ impl Iterator for KmersAndHashesIter {

let start = self.pos;
let ksize = self.ksize;
let rpos = self.end - start - 1;

// Extract the current k-mer and its reverse complement
let substr = &self.seq[start..start + ksize];
// CTB: this calculates RC each time, instead of doing so
// using a sliding window. It's easy and works, so I'm
// starting here :).
let substr_b_rc = revcomp(&self.seqb[start..start + ksize]);
let substr_rc =
std::str::from_utf8(&substr_b_rc).expect("invalid utf-8 sequence for rev comp");
let substr_rc = &self.seq_rc[rpos..rpos + ksize];

// Get the next hash value from the hasher
let hashval = self.hasher.next().expect("should not run out of hashes");
Expand All @@ -851,7 +851,7 @@ impl Iterator for KmersAndHashesIter {
} else {
substr_rc
};
// If vaild hash, return (canonical_kmer,hashval) tuple
// If valid hash, return (canonical_kmer,hashval) tuple
Some(Ok((canonical_kmer.to_string(), hashval)))
} else {
// If the hash is 0, handle based on `skip_bad_kmers`
Expand Down
Loading