Fix checking of sequence coverage

src/main.rs

@@ -7,7 +7,7 @@ const INSERTION_MARKER: &'static str = "**INSERTION**";
 const TODO_MARKER: &'static str = "**TODO**";
 
 use colored::Colorize;
-use std::collections::BTreeSet;
+use std::collections::{BTreeMap, BTreeSet};
 use std::env::Args;
 
 fn parse_command_line_arguments(mut args: Args) -> OrigamiInput {
@@ -18,7 +18,7 @@ fn parse_command_line_arguments(mut args: Args) -> OrigamiInput {
     let stapples_file_name = args.next().expect(USAGE);
 
     let scaffold_sequence = match std::fs::read_to_string(scaffold_file_name) {
-        Ok(content) => content,
+        Ok(content) => content.trim_end().to_string(),
         Err(e) => {
             panic!("Could not read scaffold sequence {e}");
         }
@@ -66,12 +66,13 @@ fn parse_staple_file(content: String) -> Vec<Staple> {
 
 fn check_coverage(input: &OrigamiInput) {
     let mut nucls: BTreeSet<usize> = (0..input.scaffold_sequence.len()).collect();
+    let mut used_by: BTreeMap<usize, (usize, Staple)> = Default::default();
     let mut success = true;
     print!("Checking coverage...");
 
-    for staple in input.staples.iter() {
+    for (staple_id, staple) in input.staples.iter().enumerate() {
         for (a, b) in staple.domains.iter().cloned() {
-            let range: Box<dyn Iterator<Item = isize>> = if b < a {
+            let range: Box<dyn Iterator<Item = isize>> = if b <= a {
                 Box::new((b as isize)..=(a as isize))
             } else {
                 Box::new((0..=(a as isize)).chain(b..(input.scaffold_sequence.len() as isize)))
@@ -80,6 +81,17 @@ fn check_coverage(input: &OrigamiInput) {
                 if !nucls.remove(&(n as usize)) {
                     success = false;
                     let msg = format!("The nucleotide {n} is used several times");
+                    println!("{}", msg.red());
+                    let dbg_msg = format!("it appears in domain [{a}, {b}]");
+                    println!("{}", dbg_msg.red())
+                }
+                if let Some(previous_staple) =
+                    used_by.insert(n as usize, (staple_id, staple.clone()))
+                {
+                    let msg = format!(
+                        "Used by {staple_id} \\ Previously used by staple {:?}",
+                        previous_staple
+                    );
                     println!("{}", msg.red())
                 }
             }
@@ -123,7 +135,7 @@ fn check_sequences(input: &OrigamiInput) {
         let stapple_chars: Vec<char> = trimed_seq.chars().collect();
         let mut stap_idx = 0;
         for (a, b) in staple.domains.iter().cloned() {
-            let range: Box<dyn Iterator<Item = isize>> = if b < a {
+            let range: Box<dyn Iterator<Item = isize>> = if b <= a {
                 Box::new(((b as isize)..=(a as isize)).rev())
             } else {
                 Box::new(
@@ -139,6 +151,7 @@ fn check_sequences(input: &OrigamiInput) {
 
                 if stap_char != expected {
                     success = false;
+                    println!("{:?}", staple);
                     let msg = format!("At pos {scaff_idx}, expected {expected}, got {stap_char}");
                     println!("{}", msg.red());
                 }
@@ -162,6 +175,7 @@ struct OrigamiInput {
     staples: Vec<Staple>,
 }
 
+#[derive(Clone, Debug)]
 struct Staple {
     domains: Vec<(isize, isize)>,
     sequence: String,