Merge pull request #36 from pangenome/fix_target_in_paf_bedpe

Fix target id

Author: AndreaGuarracino

src/impg.rs

@@ -322,7 +322,7 @@ impl Impg {
             Interval {
                 first: range_start,
                 last: range_end,
-                metadata: 0
+                metadata: target_id
             }
         ));
         if let Some(tree) = self.trees.get(&target_id) {
@@ -346,7 +346,7 @@ impl Impg {
                         Interval {
                             first: adjusted_target_start,
                             last: adjusted_target_end,
-                            metadata: 0
+                            metadata: target_id
                         }
                     );
                     results.push(adjusted_interval);
@@ -375,7 +375,7 @@ impl Impg {
             Interval {
                 first: range_start,
                 last: range_end,
-                metadata: 0
+                metadata: target_id
             }
         ));
         // Initialize stack with first query
@@ -393,13 +393,13 @@ impl Impg {
             .or_default()
             .insert((range_start, range_end));
 
-        while let Some((current_target, current_start, current_end)) = stack.pop() {
-            if let Some(tree) = self.trees.get(&current_target) {
-                tree.query(current_start, current_end, |interval| {
+        while let Some((current_target_id, current_target_start, current_target_end)) = stack.pop() {
+            if let Some(tree) = self.trees.get(&current_target_id) {
+                tree.query(current_target_start, current_target_end, |interval| {
                     let metadata = &interval.metadata;
                     let (adjusted_query_start, adjusted_query_end, adjusted_cigar, adjusted_target_start, adjusted_target_end) = 
                     project_target_range_through_alignment(
-                        (current_start, current_end),
+                        (current_target_start, current_target_end),
                         (metadata.target_start, metadata.target_end, metadata.query_start, metadata.query_end, metadata.strand),
                         &metadata.get_cigar_ops(&self.paf_file, self.paf_gzi_index.as_ref())
                     );
@@ -415,13 +415,13 @@ impl Impg {
                             Interval {
                                 first: adjusted_target_start,
                                 last: adjusted_target_end,
-                                metadata: 0
+                                metadata: current_target_id
                             }
                         );
                         results.push(adjusted_interval);
 
                         // Only add non-overlapping portions to the stack for further exploration
-                        if metadata.query_id != current_target {
+                        if metadata.query_id != current_target_id {
                             let ranges = visited_ranges.entry(metadata.query_id)
                                 .or_insert_with(|| SortedRanges::new());  // Note the closure here
 

src/main.rs

@@ -127,7 +127,7 @@ fn main() -> io::Result<()> {
 
                 if output_paf {
                     // Skip the first element (the input range) for PAF
-                    output_results_paf(&impg, results.into_iter().skip(1), &target_name, None);
+                    output_results_paf(&impg, results.into_iter().skip(1), None);
                 } else {
                     output_results_bed(&impg, results);
                 }
@@ -148,9 +148,9 @@ fn main() -> io::Result<()> {
                     // Skip the first element (the input range) for both PAF and BEDPE
                     let results_iter = results.into_iter().skip(1);
                     if output_paf {
-                        output_results_paf(&impg, results_iter, &target_name, name);
+                        output_results_paf(&impg, results_iter, name);
                     } else {
-                        output_results_bedpe(&impg, results_iter, &target_name, name);
+                        output_results_bedpe(&impg, results_iter, name);
                     }
                 }
             } else {
@@ -315,12 +315,13 @@ fn output_results_bed(impg: &Impg, results: Vec<AdjustedInterval>) {
     }
 }
 
-fn output_results_bedpe<I>(impg: &Impg, results: I, target_name: &str, name: Option<String>)
+fn output_results_bedpe<I>(impg: &Impg, results: I, name: Option<String>)
 where
     I: Iterator<Item = AdjustedInterval>
 {
     for (overlap_query, _, overlap_target) in results {
         let query_name = impg.seq_index.get_name(overlap_query.metadata).unwrap();
+        let target_name = impg.seq_index.get_name(overlap_target.metadata).unwrap();
         let (first, last, strand) = if overlap_query.first <= overlap_query.last {
             (overlap_query.first, overlap_query.last, '+')
         } else {
@@ -333,20 +334,21 @@ where
     }
 }
 
-fn output_results_paf<I>(impg: &Impg, results: I, target_name: &str, name: Option<String>)
+fn output_results_paf<I>(impg: &Impg, results: I, name: Option<String>)
 where
     I: Iterator<Item = AdjustedInterval>
 {
-    let target_length = impg.seq_index.get_len_from_id(impg.seq_index.get_id(target_name).unwrap()).unwrap();  
     for (overlap_query, cigar, overlap_target) in results {
         let query_name = impg.seq_index.get_name(overlap_query.metadata).unwrap();
+        let target_name = impg.seq_index.get_name(overlap_target.metadata).unwrap();
         let (first, last, strand) = if overlap_query.first <= overlap_query.last {
             (overlap_query.first, overlap_query.last, '+')
         } else {
             (overlap_query.last, overlap_query.first, '-')
         };
 
         let query_length = impg.seq_index.get_len_from_id(overlap_query.metadata).unwrap();  
+        let target_length = impg.seq_index.get_len_from_id(overlap_target.metadata).unwrap();  
 
         let (matches, mismatches, insertions, inserted_bp, deletions, deleted_bp, block_len) = cigar.iter().fold((0, 0, 0, 0, 0, 0, 0), |(m, mm, i, i_bp, d, d_bp, bl), op| {
             let len = op.len();