m

src/lib.rs

@@ -1,9 +1,9 @@
-use std::{time::Instant, ops::Range, collections::{HashMap, HashSet}};
+use std::{ops::Range, collections::{HashMap, HashSet}};
 use petgraph::{graph::{Graph, NodeIndex, EdgeIndex}, Undirected};
 use kseq::parse_path;
 use faimm::IndexedFasta;
 
-struct SequencesGraph {
+pub struct SequencesGraph {
     sequences: HashMap<NodeIndex, String>,
     seq_hash : HashSet<String>,
     names    : HashMap<NodeIndex, String>,
@@ -16,7 +16,7 @@ struct SequencesGraph {
     
 }
 #[derive(Debug)]
-struct Overlap {
+pub struct Overlap {
     id_a   : NodeIndex,
     range_a: Range<usize>,
     id_b   : NodeIndex,
@@ -344,7 +344,7 @@ impl SequencesGraph {
 }
 
 #[derive(Debug, Clone)]
-struct Sam {
+pub struct Sam {
     query_name : String,
     query_range: Range<usize>,
     ref_name   : String,
@@ -356,7 +356,7 @@ struct Sam {
 }
 
 impl Sam {
-    fn new(query_name: String, flag: i32, ref_name: String, ref_pos: i64, cigar: String, sequence: String, fa: &Fasta) -> Self {
+    pub fn new(query_name: String, flag: i32, ref_name: String, ref_pos: i64, cigar: String, sequence: String, fa: &Fasta) -> Self {
         let mut sequence = sequence;
         let (mut ref_range, mut query_range, ref_cigar) = matched_range(&cigar, &flag, &mut sequence);
 
@@ -377,7 +377,7 @@ impl Sam {
     }
 }
 #[derive(Debug, Clone)]
-struct NeoContig {
+pub struct NeoContig {
     sequence_id: usize,
     name: String,
     contig   : String,
@@ -387,11 +387,11 @@ struct NeoContig {
     stretch    : Vec<(NodeIndex, i32)>,
 }
 
-struct Fasta {
+pub struct Fasta {
     fa: IndexedFasta
 }
 impl Fasta {
-    fn new (path: &str) -> Self {
+    pub fn new (path: &str) -> Self {
         Fasta { fa: IndexedFasta::from_file(path).expect("Error opening fa") }
     }
     fn get_sequence (&self, contig: &str, start: usize, end: usize) -> String { // end is included