Struct SpectrumPreservingStringSet 

pub struct SpectrumPreservingStringSet { /* private fields */ }

The spectrum-preserving string set

Stores all strings in a bit-packed format with offsets to each string. This allows for both memory-efficient storage and efficient access patterns.

Offsets are stored using Elias-Fano encoding (via sux-rs) for compact representation and O(1) locate() via successor queries with Cursor.

Implementations

impl SpectrumPreservingStringSet

pub fn new(k: usize, m: usize) -> Self

Create a new empty SPSS

pub fn from_parts( strings: Vec<u8>, offsets: OffsetsVector, k: usize, m: usize, ) -> Self

Create a new SPSS from existing strings and offsets

Converts the OffsetsVector to Elias-Fano encoding for compact storage.

Arguments

• strings - Encoded string data (2-bit packed)
• offsets - Offset vector for string boundaries (will be converted to EF)
• k - K-mer size
• m - Minimizer size

pub fn string_offsets(&self, string_id: u32) -> (u64, u64)

Get the string offsets (begin, end) for a string ID

pub fn num_strings(&self) -> u64

Get the number of strings stored

pub fn string_offset(&self, string_id: u64) -> u64

Get the starting offset (in bases) of a string

pub fn k(&self) -> usize

Get the k-mer size

pub fn m(&self) -> usize

Get the minimizer size

pub fn total_bases(&self) -> u64

Get the total number of bases stored

pub fn locate(&self, absolute_pos: u64) -> Option<(u64, u64)>

Locate which string contains a given absolute position. Returns (string_id, string_begin) or None if out of bounds.

pub fn locate_with_end(&self, absolute_pos: u64) -> Option<(u64, u64, u64)>

Locate which string contains a given absolute position, returning (string_id, string_begin, string_end) in a single EF traversal. This is more efficient than calling locate() + string_offsets().

pub fn num_bits(&self) -> u64

Get memory usage in bits

pub fn strings_bytes(&self) -> usize

Get the byte size of the packed strings data

pub fn offsets_bytes(&self) -> usize

Get the byte size of the offsets vector

pub fn string_length(&self, string_id: u64) -> usize

Get the length of a specific string in bases

pub fn decode_kmer<const K: usize>( &self, string_id: u64, kmer_pos: usize, ) -> Kmer<K>

where Kmer<K>: KmerBits,

Decode a k-mer from a specific position in a string

Uses word-level loads from the packed buffer for efficiency.

pub fn decode_kmer_at<const K: usize>(&self, absolute_pos: usize) -> Kmer<K>

where Kmer<K>: KmerBits,

Decode a k-mer at an absolute base position in the concatenated strings. Avoids the need for string_id (no binary search needed). This matches the C++ util::read_kmer_at approach with decoded_offsets.

pub fn serialize_to<W: Write>(&self, writer: &mut W) -> Result<()>

Serialize the SPSS to a writer using a custom binary format.

Format:

• k: u64 (LE)
• m: u64 (LE)
• strings_len: u64 (LE)
• strings: [u8; strings_len]
• offsets: epserde Elias-Fano binary format

pub fn deserialize_from<R: Read>(reader: &mut R) -> Result<Self>

Deserialize an SPSS from a reader.

Trait Implementations

impl Debug for SpectrumPreservingStringSet

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.