Add a test for diploid blockgroups

src/models/block_group.rs

@@ -20,7 +20,6 @@ use crate::models::path::{Path, PathBlock, PathData};
 use crate::models::path_edge::PathEdge;
 use crate::models::strand::Strand;
 use crate::models::traits::*;
-use crate::test_helpers::save_graph;
 
 #[derive(Debug, Deserialize, Serialize)]
 pub struct BlockGroup {
@@ -827,9 +826,7 @@ impl BlockGroup {
 mod tests {
     use super::*;
     use crate::models::{collection::Collection, node::Node, sample::Sample, sequence::Sequence};
-    use crate::test_helpers::{
-        get_connection, interval_tree_verify, save_graph, setup_block_group,
-    };
+    use crate::test_helpers::{get_connection, interval_tree_verify, setup_block_group};
 
     #[test]
     fn test_blockgroup_create() {
@@ -1946,10 +1943,6 @@ mod tests {
     fn test_changes_against_derivative_blockgroups() {
         let conn = &get_connection(None);
         let (block_group_id, path) = setup_block_group(conn);
-        save_graph(
-            &BlockGroup::get_graph(conn, block_group_id),
-            &format!("parent_{block_group_id}.dot"),
-        );
         let new_sample = Sample::create(conn, "child");
         let new_bg_id =
             BlockGroup::get_or_create_sample_block_group(conn, "test", "child", "chr1", None)
@@ -1992,10 +1985,6 @@ mod tests {
             all_sequences,
             HashSet::from_iter(vec!["AAAAAAANNNNTTTTTCCCCCCCCCCGGGGGGGGGG".to_string(),])
         );
-        save_graph(
-            &BlockGroup::get_graph(conn, new_bg_id),
-            &format!("child_{new_bg_id}.dot"),
-        );
 
         // Now, we make a change against another descendant
         let new_sample = Sample::create(conn, "grandchild");
@@ -2042,4 +2031,114 @@ mod tests {
             HashSet::from_iter(vec!["AAAAAAANNNNTCCCCCCCCCCGGGGGGGGGG".to_string(),])
         )
     }
+
+    #[test]
+    fn test_changes_against_derivative_diploid_blockgroups() {
+        // This test ensures that if we have heterozygous changes that do not introduce frameshifts,
+        // we can modify regions downstream of them.
+        let conn = &get_connection(None);
+        let (block_group_id, path) = setup_block_group(conn);
+        let new_sample = Sample::create(conn, "child");
+        let new_bg_id =
+            BlockGroup::get_or_create_sample_block_group(conn, "test", "child", "chr1", None)
+                .unwrap();
+        let new_path = Path::query(
+            conn,
+            "select * from paths where block_group_id = ?1",
+            vec![SQLValue::from(new_bg_id)],
+        );
+        let insert_sequence = Sequence::new()
+            .sequence_type("DNA")
+            .sequence("NNNN")
+            .save(conn);
+        let insert_node_id = Node::create(conn, insert_sequence.hash.as_str(), None);
+        let insert = PathBlock {
+            id: 0,
+            node_id: insert_node_id,
+            block_sequence: insert_sequence.get_sequence(0, 4).to_string(),
+            sequence_start: 0,
+            sequence_end: 4,
+            path_start: 7,
+            path_end: 11,
+            strand: Strand::Forward,
+        };
+        let change = PathChange {
+            block_group_id: new_bg_id,
+            path: new_path[0].clone(),
+            path_accession: None,
+            start: 7,
+            end: 11,
+            block: insert,
+            chromosome_index: 1,
+            phased: 0,
+        };
+        // note we are making our change against the new blockgroup, and not the parent blockgroup
+        let tree = BlockGroup::intervaltree_for(conn, new_bg_id, true);
+        BlockGroup::insert_change(conn, &change, &tree);
+        let all_sequences = BlockGroup::get_all_sequences(conn, new_bg_id, true);
+        assert_eq!(
+            all_sequences,
+            HashSet::from_iter(vec![
+                "AAAAAAANNNNTTTTTTTTTCCCCCCCCCCGGGGGGGGGG".to_string(),
+                "AAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGG".to_string(),
+            ])
+        );
+
+        // Now, we make a change against another descendant
+        let new_sample = Sample::create(conn, "grandchild");
+        let gc_bg_id = BlockGroup::get_or_create_sample_block_group(
+            conn,
+            "test",
+            "grandchild",
+            "chr1",
+            Some("child"),
+        )
+        .unwrap();
+        let new_path = Path::query(
+            conn,
+            "select * from paths where block_group_id = ?1",
+            vec![SQLValue::from(gc_bg_id)],
+        );
+
+        let insert_sequence = Sequence::new()
+            .sequence_type("DNA")
+            .sequence("NNNN")
+            .save(conn);
+        let insert_node_id =
+            Node::create(conn, insert_sequence.hash.as_str(), "new-hash".to_string());
+
+        let insert = PathBlock {
+            id: 0,
+            node_id: insert_node_id,
+            block_sequence: insert_sequence.get_sequence(0, 4).to_string(),
+            sequence_start: 0,
+            sequence_end: 4,
+            path_start: 20,
+            path_end: 24,
+            strand: Strand::Forward,
+        };
+        let change = PathChange {
+            block_group_id: gc_bg_id,
+            path: new_path[0].clone(),
+            path_accession: None,
+            start: 20,
+            end: 24,
+            block: insert,
+            chromosome_index: 1,
+            phased: 0,
+        };
+        // take out an entire block.
+        let tree = BlockGroup::intervaltree_for(conn, gc_bg_id, true);
+        BlockGroup::insert_change(conn, &change, &tree);
+        let all_sequences = BlockGroup::get_all_sequences(conn, gc_bg_id, true);
+        assert_eq!(
+            all_sequences,
+            HashSet::from_iter(vec![
+                "AAAAAAANNNNTTTTTTTTTCCCCCCCCCCGGGGGGGGGG".to_string(),
+                "AAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGG".to_string(),
+                "AAAAAAAAAATTTTTTTTTTNNNNCCCCCCGGGGGGGGGG".to_string(),
+                "AAAAAAANNNNTTTTTTTTTNNNNCCCCCCGGGGGGGGGG".to_string()
+            ])
+        )
+    }
 }