Version 0.3.1

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "awry"
-version = "0.3.0"
+version = "0.3.1"
 description = "Library for creating FM-indexes from FASTA/FASTQ files. AWRY is able to search at lightning speed by leveraging SIMD vectorization and multithreading over collections of queries."
 license = "BSD-3-Clause"
 homepage = "https://github.com/UM-Applied-Algorithms-Lab/AWRY_Index"

src/search.rs

@@ -4,49 +4,51 @@ use serde::{Deserialize, Serialize};
 use crate::{alphabet::Symbol, fm_index::FmIndex};
 
 /// Type representing a position in the BWT
-pub (crate)  type SearchPtr = u64;
+pub(crate) type SearchPtr = u64;
 
-/// Represents the range in the BWT that corresponds to a query. A range is valid (corresponds to at 
+/// Represents the range in the BWT that corresponds to a query. A range is valid (corresponds to at
 /// least one position) as long as start_ptr <= end_ptr
-/// 
+///
 /// # Example
 /// ```no_run
 /// use awry::search::SearchRange;
 /// use awry::alphabet::{SymbolAlphabet, Symbol};
 /// use awry::fm_index::FmIndex;;
 /// use std::path::Path;
-/// 
+///
 /// let fm_index = FmIndex::load(&Path::new("test.awry")).expect("unable to load fm index from file");
 /// let search_range = SearchRange::new(&fm_index, Symbol::new_ascii(SymbolAlphabet::Nucleotide, 'A'));
 /// ```
-#[derive(Clone, Serialize, Deserialize, Debug, PartialEq, PartialOrd, Eq, Ord, Hash, Default, MemSize)]
+#[derive(
+    Clone, Serialize, Deserialize, Debug, PartialEq, PartialOrd, Eq, Ord, Hash, Default, MemSize,
+)]
 pub struct SearchRange {
     pub start_ptr: SearchPtr,
     pub end_ptr: SearchPtr,
 }
 
 impl SearchRange {
     /// Creates a new SearchRange, representing all positions in the BWT
-    /// 
+    ///
     /// # Example
     /// ```no_run
     /// use awry::fm_index::{FmIndex, FmBuildArgs};
     /// use awry::alphabet::{SymbolAlphabet, Symbol};
     /// use awry::search::SearchRange;
     /// use std::path::Path;
-    /// 
+    ///
     /// let fm_index = FmIndex::load(&Path::new("test.awry")).expect("unable to load fm index from file");
     /// let search_range = SearchRange::new(&fm_index, Symbol::new_ascii(SymbolAlphabet::Nucleotide, 'A'));
     /// ```
-    pub fn new(fm_index: &FmIndex, symbol:Symbol) -> Self {
+    pub fn new(fm_index: &FmIndex, symbol: Symbol) -> Self {
         SearchRange {
             start_ptr: fm_index.prefix_sums()[symbol.index() as usize] as SearchPtr,
-            end_ptr: fm_index.prefix_sums()[(symbol.index()+1) as usize]  - 1 as SearchPtr,
+            end_ptr: fm_index.prefix_sums()[(symbol.index() + 1) as usize] - 1 as SearchPtr,
         }
     }
 
     /// Creates a new SearchRange, representing an invalid range (i.e., no elements)
-    pub  (crate) fn zero() -> Self {
+    pub fn zero() -> Self {
         SearchRange {
             start_ptr: 1,
             end_ptr: 0,
@@ -55,13 +57,13 @@ impl SearchRange {
 
     ///returns true if the search range doesn't represent any elements.
     #[inline]
-    pub  (crate) fn is_empty(&self) -> bool {
+    pub fn is_empty(&self) -> bool {
         return self.start_ptr > self.end_ptr;
     }
 
     ///gets the number of elements represented by the search range
     #[inline]
-    pub  (crate) fn len(&self) -> SearchPtr {
+    pub fn len(&self) -> SearchPtr {
         match self.is_empty() {
             true => 0,
             false => self.end_ptr - self.start_ptr + 1,
@@ -70,7 +72,7 @@ impl SearchRange {
 
     /// Returns an interator over the BWT positions corresponding to this search range
     #[inline]
-    pub  (crate) fn range_iter(&self) -> core::ops::Range<SearchPtr> {
+    pub fn range_iter(&self) -> core::ops::Range<SearchPtr> {
         match self.is_empty() {
             true => 0..0,
             false => self.start_ptr..(self.end_ptr + 1),