Merge pull request #44 from pangenome/avoid_short_chunks

max_depth as u16 to reduce memory usage

src/impg.rs

@@ -396,7 +396,7 @@ impl Impg {
         range_start: i32, 
         range_end: i32,
         masked_regions: Option<&FxHashMap<u32, SortedRanges>>,
-        max_depth: i32,
+        max_depth: u16,
         min_transitive_region_size: i32,
         min_distance_between_ranges: i32,
     ) -> Vec<AdjustedInterval> {
@@ -416,7 +416,7 @@ impl Impg {
             }
         ));
         // Initialize stack with first query
-        let mut stack = vec![(target_id, range_start, range_end, 0i32)];
+        let mut stack = vec![(target_id, range_start, range_end, 0u16)];
         // Initialize visited ranges from masked regions if provided
         let mut visited_ranges: FxHashMap<u32, SortedRanges> = if let Some(m) = masked_regions {
             m.iter()

src/main.rs

@@ -58,7 +58,7 @@ enum Args {
 
         /// Maximum recursion depth for transitive overlaps (0 for no limit)
         #[clap(short = 'm', long, value_parser, default_value_t = 1)]
-        max_depth: i32,
+        max_depth: u16,
 
         /// Minimum size of intervals to consider for transitive queries
         #[clap(long, value_parser, default_value_t = 500)]
@@ -91,7 +91,7 @@ enum Args {
 
         /// Maximum recursion depth for transitive overlaps (0 for no limit)
         #[clap(short = 'm', long, value_parser, default_value_t = 1)]
-        max_depth: i32,
+        max_depth: u16,
 
         /// Minimum size of intervals to consider for transitive queries
         #[clap(long, value_parser, default_value_t = 0)]
@@ -330,7 +330,7 @@ fn perform_query(
     target_name: &str, 
     target_range: (i32, i32), 
     transitive: bool,
-    max_depth: i32,
+    max_depth: u16,
     min_transitive_region_size: i32,
     min_distance_between_ranges: i32
 ) -> Vec<AdjustedInterval> {

src/partition.rs

@@ -14,7 +14,7 @@ pub fn partition_alignments(
     sequence_prefix: &str,
     min_region_size: i32,
     merge_distance: i32,
-    max_depth: i32,
+    max_depth: u16,
     min_transitive_region_size: i32,
     min_distance_between_ranges: i32,
     min_mask_proximity: i32,