Enable updates to blockgroups

Cargo.toml

@@ -26,6 +26,7 @@ serde_json = "1.0.128"
 sha2 = "0.10.8"
 tempfile = "3.12.0"
 tempdir = "0.3.7"
+interavl = "0.2.0"
 
 [dev-dependencies]
 cargo-llvm-cov = "0.6.13"

src/exports/gfa.rs

@@ -1,11 +1,4 @@
-use itertools::Itertools;
-use petgraph::prelude::DiGraphMap;
-use rusqlite::{types::Value as SQLValue, Connection};
-use std::collections::{HashMap, HashSet};
-use std::fs::File;
-use std::io::{BufWriter, Write};
-use std::path::PathBuf;
-
+use crate::graph::{GraphEdge, GraphNode};
 use crate::models::{
     block_group::BlockGroup,
     block_group_edge::BlockGroupEdge,
@@ -16,6 +9,13 @@ use crate::models::{
     path_edge::PathEdge,
     strand::Strand,
 };
+use itertools::Itertools;
+use petgraph::prelude::DiGraphMap;
+use rusqlite::{types::Value as SQLValue, Connection};
+use std::collections::{HashMap, HashSet};
+use std::fs::File;
+use std::io::{BufWriter, Write};
+use std::path::PathBuf;
 
 pub fn export_gfa(
     conn: &Connection,
@@ -104,12 +104,14 @@ fn segment_line(sequence: &str, node_id: i64, sequence_start: i64) -> String {
 
 fn write_links(
     writer: &mut BufWriter<File>,
-    graph: &DiGraphMap<i64, ()>,
+    graph: &DiGraphMap<GraphNode, GraphEdge>,
     edges_by_node_pair: &HashMap<(i64, i64), Edge>,
     node_sequence_starts_by_end_coordinate: HashMap<(i64, i64), i64>,
 ) {
-    for (source, target, ()) in graph.all_edges() {
-        let edge = edges_by_node_pair.get(&(source, target)).unwrap();
+    for (source, target, edge_weight) in graph.all_edges() {
+        let edge = edges_by_node_pair
+            .get(&(source.node_id, target.node_id))
+            .unwrap();
         if Node::is_terminal(edge.source_node_id) || Node::is_terminal(edge.target_node_id) {
             continue;
         }
@@ -135,7 +137,7 @@ fn write_links(
             .unwrap_or_else(|_| {
                 panic!(
                     "Error writing link from segment {} to {} to GFA stream",
-                    source, target,
+                    source.node_id, target.node_id,
                 )
             });
     }

src/graph.rs

@@ -41,6 +41,27 @@ where
     })
 }
 
+#[derive(Clone, Copy, Debug, Eq, PartialEq, Hash, Ord, PartialOrd)]
+pub struct GraphNode {
+    pub block_id: i64,
+    pub node_id: i64,
+    pub sequence_start: i64,
+    pub sequence_end: i64,
+}
+
+impl GraphNode {
+    pub fn length(&self) -> i64 {
+        self.sequence_end - self.sequence_start
+    }
+}
+
+#[derive(Clone, Copy, Debug, Eq, PartialEq, Hash, Ord, PartialOrd)]
+pub struct GraphEdge {
+    pub edge_id: i64,
+    pub chromosome_index: i64,
+    pub phased: i64,
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;
@@ -161,4 +182,46 @@ mod tests {
             HashSet::from_iter(expected_paths)
         );
     }
+
+    #[test]
+    fn test_ultra_bubble_path() {
+        // This graph looks like this:
+        //              8
+        //            /  \
+        //          6  -> 7
+        //         /        \
+        //    1 -> 2 -> 3 -> 4 -> 5
+        //
+        //  We ensure that we capture all 3 paths from 1 -> 5
+        let mut graph: DiGraphMap<i64, ()> = DiGraphMap::new();
+        graph.add_node(1);
+        graph.add_node(2);
+        graph.add_node(3);
+        graph.add_node(4);
+        graph.add_node(5);
+        graph.add_node(6);
+        graph.add_node(7);
+        graph.add_node(8);
+        graph.add_node(9);
+
+        graph.add_edge(1, 2, ());
+        graph.add_edge(2, 3, ());
+        graph.add_edge(3, 4, ());
+        graph.add_edge(4, 5, ());
+        graph.add_edge(2, 6, ());
+        graph.add_edge(6, 7, ());
+        graph.add_edge(7, 4, ());
+        graph.add_edge(6, 8, ());
+        graph.add_edge(8, 7, ());
+
+        let paths = all_simple_paths(&graph, 1, 5).collect::<Vec<Vec<i64>>>();
+        assert_eq!(
+            HashSet::<Vec<i64>>::from_iter::<Vec<Vec<i64>>>(paths),
+            HashSet::from_iter(vec![
+                vec![1, 2, 3, 4, 5],
+                vec![1, 2, 6, 7, 4, 5],
+                vec![1, 2, 6, 8, 7, 4, 5]
+            ])
+        );
+    }
 }