Fixes after rebase; address comment

src/exports/gfa.rs

@@ -477,7 +477,7 @@ mod tests {
             chromosome_index: 1,
             phased: 0,
         };
-        let tree = Path::intervaltree_for(&conn, &path);
+        let tree = path.intervaltree(&conn);
         BlockGroup::insert_change(&conn, &change, &tree);
 
         let edges = BlockGroupEdge::edges_for_block_group(&conn, block_group_id);

src/models/edge.rs

@@ -815,7 +815,7 @@ mod tests {
             chromosome_index: 1,
             phased: 0,
         };
-        let tree = Path::intervaltree_for(&conn, &path);
+        let tree = path.intervaltree(&conn);
         BlockGroup::insert_change(&conn, &change, &tree);
         let mut edges = BlockGroupEdge::edges_for_block_group(&conn, block_group_id);
 

src/models/path.rs

@@ -473,7 +473,7 @@ impl Path {
                 false,
             )
         } else {
-            first_mapping.target_range.start
+            Ok(first_mapping.target_range.start)
         };
 
         let translated_end = if last_mapping.source_range.contains(end) {
@@ -484,13 +484,17 @@ impl Path {
                 false,
             )
         } else {
-            last_mapping.target_range.end
+            Ok(last_mapping.target_range.end)
         };
 
+        if translated_start.is_err() || translated_end.is_err() {
+            return None;
+        }
+
         Some(Annotation {
             name: annotation.name,
-            start: translated_start,
-            end: translated_end,
+            start: translated_start.expect("Failed to translate start"),
+            end: translated_end.expect("Failed to translate end"),
         })
     }
 

src/range.rs

@@ -182,13 +182,17 @@ impl Range {
         range2: &Range,
         sequence_length: i64,
         is_circular_contig: bool,
-    ) -> i64 {
+    ) -> Result<i64, &'static str> {
         if !self.contains(index) {
-            panic!("Index {} is not contained in range {:?}", index, self);
+            return Err("Index is not contained in range");
         }
 
         let offset = index - self.start;
-        Range::circular_mod(range2.start + offset, sequence_length, is_circular_contig)
+        Ok(Range::circular_mod(
+            range2.start + offset,
+            sequence_length,
+            is_circular_contig,
+        ))
     }
 }
 

src/updates/library.rs

@@ -106,7 +106,7 @@ pub fn update_with_library(
         parts_list.push(parts_by_index.get(&index).unwrap());
     }
 
-    let path_intervaltree = Path::intervaltree_for(conn, &path);
+    let path_intervaltree = path.intervaltree(conn);
     let start_blocks: Vec<_> = path_intervaltree
         .query_point(start_coordinate)
         .map(|x| &x.value)