Fix bigBed zooms with overlapping regions

Author: jackh726

bigtools/src/bbi/bbiwrite.rs

@@ -769,6 +769,7 @@ pub(crate) fn write_vals<
             .take(options.max_zooms as usize)
             .collect(),
     };
+    let zoom_sizes: Vec<u32> = zoom_sizes.into_iter().filter(|z| *z != 0).collect();
     let zooms_map: BTreeMap<u32, ZoomValue> = zoom_sizes.iter().copied().map(make_zoom).collect();
 
     let mut chrom_ids = IdMap::default();

bigtools/src/bbi/bigbedwrite.rs

@@ -439,17 +439,32 @@ async fn process_val_zoom(
             }
         }
 
+        // At this point, if there is are any items in the list, the end of the
+        // last item must overlap or come up to the current item start
         debug_assert!(overlap
             .get_last()
             .map(|o| o.end >= item_start)
             .unwrap_or(true));
 
-        if overlap.get_last().map(|o| o.end).unwrap_or(item_start) == item_start {
-            overlap.insert_last(Value {
-                start: item_start,
-                end: item_end,
-                value: 1.0,
-            });
+        // If the current item extends past the last item (or if there are no
+        // previous items), we must add one
+        match overlap.get_last() {
+            Some(o) => {
+                if o.end < item_end {
+                    overlap.insert_last(Value {
+                        start: o.end,
+                        end: item_end,
+                        value: 1.0,
+                    });
+                }
+            }
+            None => {
+                overlap.insert_last(Value {
+                    start: item_start,
+                    end: item_end,
+                    value: 1.0,
+                });
+            }
         }
 
         let next_start = next_val.map(|v| v.start).unwrap_or(u32::max_value());

bigtools/src/utils/cli/bigbedtobed.rs

@@ -114,7 +114,7 @@ pub fn write_bed_singlethreaded<R: Reopen + SeekableRead>(
     let chroms: Vec<ChromInfo> = if let Some(arg_chrom) = chrom {
         let chrom = bigbed.chroms().iter().find(|c| c.name == arg_chrom);
         let Some(chrom) = chrom else {
-            eprintln!("{arg_chrom} not found in file.");
+            eprintln!("Error: {arg_chrom} not found in file.");
             return Ok(());
         };
         vec![chrom.clone()]
@@ -124,13 +124,19 @@ pub fn write_bed_singlethreaded<R: Reopen + SeekableRead>(
     let mut writer = io::BufWriter::with_capacity(32 * 1000, out_file);
     let mut buf: String = String::with_capacity(50); // Estimate
     if let Some(zoom) = zoom {
+        if bigbed
+            .info()
+            .zoom_headers
+            .iter()
+            .all(|z| z.reduction_level != zoom)
+        {
+            eprintln!("Error: Zoom level not found: {zoom}");
+            return Ok(());
+        }
         for chrom in chroms {
             let start = start.unwrap_or(0);
             let end = end.unwrap_or(chrom.length);
-            for raw_val in bigbed
-                .get_zoom_interval(&chrom.name, start, end, zoom)
-                .unwrap()
-            {
+            for raw_val in bigbed.get_zoom_interval(&chrom.name, start, end, zoom)? {
                 let val = raw_val?;
                 uwrite!(
                     &mut buf,