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use sa::{insert, suffix_array}; use std::ops::Index; /// Generate the [Burrows-Wheeler Transform](https://en.wikipedia.org/wiki/Burrows%E2%80%93Wheeler_transform) /// of the given input. /// /// ``` rust /// let text = String::from("The quick brown fox jumps over the lazy dog"); /// let bw = nucleic_acid::bwt(text.as_bytes()); /// assert_eq!(String::from("gkynxeser\u{0}l i hhv otTu c uwd rfm ebp qjoooza"), /// String::from_utf8(bw).unwrap()); /// ``` /// The output can then be used for compression or FM-index'ing. pub fn bwt(input: &[u8]) -> Vec<u8> { suffix_array(input).into_iter().map(|i| { // BWT[i] = S[SA[i] - 1] if i == 0 { 0 } else { input[(i - 1) as usize] } }).collect() } // Takes a frequency map of bytes and generates the index of first occurrence // of each byte. fn generate_occurrence_index(map: &mut Vec<u32>) { let mut idx = 0; for i in 0..map.len() { let c = map[i]; map[i] = idx; idx += c; } } /// Invert the BWT and generate the original data. /// /// ``` rust /// let text = String::from("Hello, world!"); /// let bw = nucleic_acid::bwt(text.as_bytes()); /// let ibw = nucleic_acid::ibwt(&bw); /// assert_eq!(text, String::from_utf8(ibw).unwrap()); /// ``` pub fn ibwt(input: &[u8]) -> Vec<u8> { // get the byte distribution let mut map = Vec::new(); for i in input { insert(&mut map, *i); } generate_occurrence_index(&mut map); // generate the LF vector let mut lf = vec![0; input.len()]; for (i, c) in input.iter().enumerate() { let byte = *c as usize; let val = map[byte]; lf[i] = val; map[byte] = val + 1; } let mut idx = 0; // construct the sequence by traversing through the LF vector let mut output = vec![0; input.len()]; for i in (0..(input.len() - 1)).rev() { output[i] = input[idx]; idx = lf[idx] as usize; } output.pop(); output } /// [Ferragina-Manzini index](https://en.wikipedia.org/wiki/FM-index) /// (or Full-text index in Minute space) for finding occurrences of substrings /// in O(1) time. /// /// ``` rust /// use nucleic_acid::FMIndex; /// /// let text = String::from("GCGTGCCCAGGGCACTGCCGCTGCAGGCGTAGGCATCGCATCACACGCGT"); /// let index = FMIndex::new(text.as_bytes()); /// /// // count the occurrences /// assert_eq!(0, index.count("CCCCC")); /// assert_eq!(3, index.count("TG")); /// /// // ... or get their positions /// assert_eq!(index.search("GCGT"), vec![46, 26, 0]); /// ``` /// /// The current implementation of FM-index is a memory killer, since it stores positions /// of **all bytes** in the given data. For the human genome (~3 GB), it consumed /// ~27 GB of RAM to build the index (in ~4 mins). /// /// That said, it still returns the match results in a few microseconds. #[derive(Clone, Debug)] pub struct FMIndex { /// BW-transformed data data: Vec<u8>, /// forward frequency of each character in the BWT data cache: Vec<u32>, /// incremental character frequencies occ_map: Vec<u32>, /// LF-mapping for backward search lf_vec: Vec<u32>, } impl FMIndex { /// Generate an FM-index for the input data. #[inline] pub fn new(data: &[u8]) -> FMIndex { FMIndex::new_from_bwt(bwt(data)) } /// Get the reference to the inner BWT data. /// /// Note that the length of BWT is one more than the length of the actual text, /// since it has a null byte to indicate empty string. pub fn bwt(&self) -> &[u8] { &self.data } /// Generate the FM-index from the BWT data. /// /// It's not a good idea to generate FM-index from scratch all the time, especially for large inputs. /// This would be very useful when your data is large and remains constant for a while. /// /// FM-index internally uses BWT, and BWT is generated from the suffix array, which takes a lot of time. /// If your input doesn't change, then it's better to get the BWT data (using `bwt` method), write it /// to a file and generate the index from that in the future. pub fn new_from_bwt(bwt_data: Vec<u8>) -> FMIndex { let mut map = Vec::new(); let mut count = vec![0u32; bwt_data.len()]; let mut idx = 0; // generate the frequency map and forward frequency vector from BWT for i in &bwt_data { let value = insert(&mut map, *i); count[idx] = value; idx += 1; } generate_occurrence_index(&mut map); let mut lf_vec = count.clone(); let mut lf_occ_map = map.clone(); // generate the LF vector (just like inverting the BWT) for (i, c) in bwt_data.iter().enumerate() { let idx = *c as usize; lf_vec[i] = lf_occ_map[idx]; lf_occ_map[idx] += 1; } let mut i = lf_vec[0] as usize; lf_vec[0] = 0; let mut counter = bwt_data.len() as u32 - 1; // Only difference is that we replace the LF indices with the lengths of prefix // from a particular position (in other words, the number of times // it would take us to get to the start of string). for _ in 0..(bwt_data.len() - 1) { let next = lf_vec[i]; lf_vec[i] = counter; i = next as usize; counter -= 1; } FMIndex { data: bwt_data, cache: count, occ_map: map, lf_vec: lf_vec, } } /// Get the nearest position of a character in the internal BWT data. /// /// The `count` and `search` methods rely on this method for finding occurrences. /// For example, we can do soemthing like this, /// /// ``` rust /// use nucleic_acid::FMIndex; /// let fm = FMIndex::new(b"Hello, Hello, Hello" as &[u8]); /// /// // initially, the range should be the length of the BWT /// let mut top = 0; /// let mut bottom = fm.bwt().len(); /// let query = b"llo"; /// /// // feed the characters in the reverse /// for ch in query.iter().rev() { /// top = fm.nearest(top, *ch); /// bottom = fm.nearest(bottom, *ch); /// if top >= bottom { /// return /// } /// } /// /// // If we get a valid range, then everything in that range is a valid match. /// // This way, we can get both the count and positions... /// assert_eq!(3, bottom - top); /// assert_eq!(vec![17, 10, 3], (top..bottom).map(|i| fm[i]).collect::<Vec<_>>()); /// ``` /// /// This is backward searching. As you feed in the characters along with a position, `nearest` will /// give you a new position in the index. Once the range becomes invalid (which happens when the /// substring doesn't exist), we can bail out. On the contrary, if the range remains valid after /// you've fed in all the characters, then every value within in that range is an occurrence. /// /// So, this is useful when you want to cache the repeating ranges. With this, you can build your own /// count/search functions with caching. It's also useful for making custom approximate matching functions /// by backtracking whenever there's an invalid range. pub fn nearest(&self, idx: usize, ch: u8) -> usize { match self.occ_map.get(ch as usize) { Some(res) if *res > 0 => { *res as usize + (0..idx).rev() .find(|&i| self.data[i] == ch) .map(|i| self.cache[i] as usize) .unwrap_or(0) }, _ => 0, } } fn get_range(&self, query: &str) -> Option<(usize, usize)> { let mut top = 0; let mut bottom = self.data.len(); for ch in query.as_bytes().iter().rev() { top = self.nearest(top, *ch); bottom = self.nearest(bottom, *ch); if top >= bottom { return None } } if top >= bottom { None } else { Some((top, bottom)) } } /// Count the occurrences of the substring in the original data. pub fn count(&self, query: &str) -> usize { match self.get_range(query) { Some((top, bottom)) => bottom - top, None => 0, } } /// Get the positions of occurrences of substring in the original data. pub fn search(&self, query: &str) -> Vec<usize> { match self.get_range(query) { Some((top, bottom)) => (top..bottom).map(|idx| { let i = self.nearest(idx, self.data[idx]); self.lf_vec[i] as usize }).collect(), None => Vec::new(), } } } impl Index<usize> for FMIndex { type Output = u32; fn index(&self, i: usize) -> &u32 { self.lf_vec.get(i).expect("index out of range") } } #[cfg(test)] mod tests { use super::{FMIndex, bwt, ibwt}; #[test] fn test_bwt_and_ibwt() { let text = String::from("ATCTAGGAGATCTGAATCTAGTTCAACTAGCTAGATCTAGAGACAGCTAA"); let bw = bwt(text.as_bytes()); let ibw = ibwt(&bw); assert_eq!(String::from("AATCGGAGTTGCTTTG\u{0}AGTAGTGATTTTAAGAAAAAACCCCCCTAAAACG"), String::from_utf8(bw).unwrap()); assert_eq!(text, String::from_utf8(ibw).unwrap()); } #[test] fn test_fm_index() { let text = String::from("GCGTGCCCAGGGCACTGCCGCTGCAGGCGTAGGCATCGCATCACACGCGT"); let index = FMIndex::new(text.as_bytes()); assert_eq!(0, index.count("CCCCC")); let mut result = index.search("TG"); result.sort(); assert_eq!(result, vec![3, 15, 21]); let mut result = index.search("GCGT"); result.sort(); assert_eq!(result, vec![0, 26, 46]); assert_eq!(vec![1], index.search("CGTGCCC")); } }