all i32

src/impg.rs

@@ -396,9 +396,9 @@ impl Impg {
         range_start: i32, 
         range_end: i32,
         masked_regions: Option<&FxHashMap<u32, SortedRanges>>,
-        max_depth: u16,
-        min_interval_size: u32,
-        min_distance_between_ranges: u32,
+        max_depth: i32,
+        min_interval_size: i32,
+        min_distance_between_ranges: i32,
     ) -> Vec<AdjustedInterval> {
         let mut results = Vec::new();
         // Add the input range to the results
@@ -416,7 +416,7 @@ impl Impg {
             }
         ));
         // Initialize stack with first query
-        let mut stack = vec![(target_id, range_start, range_end, 0u16)];
+        let mut stack = vec![(target_id, range_start, range_end, 0i32)];
         // Initialize visited ranges from masked regions if provided
         let mut visited_ranges: FxHashMap<u32, SortedRanges> = if let Some(m) = masked_regions {
             m.iter()
@@ -488,14 +488,14 @@ impl Impg {
                                 if idx > 0 {
                                     // Check previous range
                                     let (_, prev_end) = ranges.ranges[idx - 1];
-                                    if ((new_min - prev_end).abs() as u32) < min_distance_between_ranges {
+                                    if (new_min - prev_end).abs() < min_distance_between_ranges {
                                         should_add = false;
                                     }
                                 }
                                 if should_add && idx < ranges.ranges.len() {
                                     // Check next range
                                     let (next_start, _) = ranges.ranges[idx];
-                                    if ((next_start - new_max).abs() as u32) < min_distance_between_ranges {
+                                    if (next_start - new_max).abs() < min_distance_between_ranges {
                                         should_add = false;
                                     }
                                 }
@@ -506,7 +506,7 @@ impl Impg {
 
                                 // Add non-overlapping portions to stack
                                 for (new_start, new_end) in new_ranges {
-                                    if ((new_end - new_start).abs() as u32) >= min_interval_size {
+                                    if (new_end - new_start).abs() >= min_interval_size {
                                         stack.push((metadata.query_id, new_start, new_end, current_depth + 1));
                                     }
                                 }

src/main.rs

@@ -50,23 +50,23 @@ enum Args {
 
         /// Maximum distance between intervals to merge.
         #[clap(short = 'd', long, value_parser, default_value_t = 10000)]
-        merge_distance: usize,
+        merge_distance: i32,
 
         /// Minimum length for intervals.
         #[clap(short = 'l', long, value_parser, default_value_t = 5000)]
-        min_length: usize,
+        min_length: i32,
 
         /// Maximum recursion depth for transitive overlaps (0 for no limit).
         #[clap(short = 'm', long, value_parser, default_value_t = 1)]
-        max_depth: u16,
+        max_depth: i32,
 
         /// Minimum size of intervals to consider for transitive queries
         #[clap(long, value_parser, default_value_t = 0)]
-        min_interval_size: u32,
+        min_interval_size: i32,
 
         /// Minimum distance between transitive ranges to consider on the same sequence
         #[clap(long, value_parser, default_value_t = 0)]
-        min_distance_between_ranges: u32,
+        min_distance_between_ranges: i32,
     },
     /// Query overlaps in the alignment.
     Query {
@@ -87,15 +87,15 @@ enum Args {
 
         /// Maximum recursion depth for transitive overlaps (0 for no limit).
         #[clap(short = 'm', long, value_parser, default_value_t = 1)]
-        max_depth: u16,
+        max_depth: i32,
 
         /// Minimum size of intervals to consider for transitive queries
         #[clap(long, value_parser, default_value_t = 0)]
-        min_interval_size: u32,
+        min_interval_size: i32,
 
         /// Minimum distance between transitive ranges to consider on the same sequence
         #[clap(long, value_parser, default_value_t = 0)]
-        min_distance_between_ranges: u32,
+        min_distance_between_ranges: i32,
 
         /// Output results in PAF format.
         #[clap(short = 'P', long, action)]
@@ -325,9 +325,9 @@ fn perform_query(
     target_name: &str, 
     target_range: (i32, i32), 
     transitive: bool,
-    max_depth: u16,
-    min_interval_size: u32,
-    min_distance_between_ranges: u32
+    max_depth: i32,
+    min_interval_size: i32,
+    min_distance_between_ranges: i32
 ) -> Vec<AdjustedInterval> {
     let (target_start, target_end) = target_range;
     let target_id = impg.seq_index.get_id(target_name).expect("Target name not found in index");

src/partition.rs

@@ -12,11 +12,11 @@ pub fn partition_alignments(
     impg: &Impg,
     window_size: usize,
     sequence_prefix: &str,
-    min_length: usize,
-    merge_distance: usize,
-    max_depth: u16,
-    min_interval_size: u32,
-    min_distance_between_ranges: u32,
+    min_length: i32,
+    merge_distance: i32,
+    max_depth: i32,
+    min_interval_size: i32,
+    min_distance_between_ranges: i32,
     debug: bool,
 ) -> io::Result<()> {
     // Get all sequences with the given prefix
@@ -128,7 +128,7 @@ pub fn partition_alignments(
             // Ignore CIGAR strings and target intervals.
             debug!("  Merging overlaps closer than {}bp", merge_distance); // bedtools sort | bedtools merge -d merge_distance
             //let merge_start = Instant::now();
-            merge_overlaps(&mut overlaps, merge_distance as i32);
+            merge_overlaps(&mut overlaps, merge_distance);
             //let merge_time = merge_start.elapsed();
             debug!("  Collected {} query overlaps after merging", overlaps.len());