From 5543a8138674e4665f149c7955c30462647c93b7 Mon Sep 17 00:00:00 2001
From: OfficialBishal <bishal.modern@gmail.com>
Date: Thu, 25 Jun 2026 07:55:07 -0400
Subject: [PATCH] fix: assign_view drop_unassigned no longer drops rows with
 NaNs in other columns

assign_view(drop_unassigned=True) dropped every row containing a NaN in any column, so intervals that were assigned to a view region were lost if they had a NaN in an unrelated column (e.g. cooler bins with missing weights). Only drop intervals whose view assignment is NaN, and add a regression test.

Closes #160
---
 CHANGES.md          |  5 +++++
 src/bioframe/ops.py |  4 +++-
 tests/test_ops.py   | 21 +++++++++++++++++++++
 3 files changed, 29 insertions(+), 1 deletion(-)

diff --git a/CHANGES.md b/CHANGES.md
index 5c466d6d..91c6ffb7 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -2,6 +2,11 @@
 
 ## [Upcoming release](https://github.com/open2c/bioframe/compare/v0.8.0...HEAD)
 
+Bug fixes:
+
+- `assign_view(..., drop_unassigned=True)` now drops only intervals that fall outside the view,
+  instead of also dropping rows that contain NaNs in unrelated columns.
+
 ## v0.8.0
 
 Date: 2025-04-08
diff --git a/src/bioframe/ops.py b/src/bioframe/ops.py
index 934603d8..82cab563 100644
--- a/src/bioframe/ops.py
+++ b/src/bioframe/ops.py
@@ -1893,7 +1893,9 @@ def assign_view(
     out_df.rename(columns={view_name_col + "_view": df_view_col}, inplace=True)
 
     if drop_unassigned:
-        out_df = out_df.iloc[pd.isna(out_df).any(axis=1).values == 0, :]
+        # only drop intervals that weren't assigned to a view region, not rows
+        # that happen to contain NaNs in other columns
+        out_df = out_df[pd.notna(out_df[df_view_col]).values]
     out_df.reset_index(inplace=True, drop=True)
 
     return_cols = [*list(df.columns), df_view_col]
diff --git a/tests/test_ops.py b/tests/test_ops.py
index 66c0fd2a..f0f662d3 100644
--- a/tests/test_ops.py
+++ b/tests/test_ops.py
@@ -2289,3 +2289,24 @@ def test_sort_bedframe():
     assert (
         df.dtypes == bioframe.sort_bedframe(df, view_df, view_name_col="fruit").dtypes
     ).all()
+
+
+def test_assign_view_drop_unassigned_keeps_nan_in_other_columns():
+    # drop_unassigned should only drop intervals that fall outside the view, not
+    # intervals that merely contain NaNs in unrelated columns (e.g. cooler bins with
+    # missing weights). See open2c/bioframe#160.
+    view_df = bioframe.make_viewframe([("chr1", 0, 100, "region1")])
+    df = pd.DataFrame(
+        {
+            "chrom": ["chr1", "chr1", "chr2"],
+            "start": [10, 30, 10],
+            "end": [20, 40, 20],
+            "value": [np.nan, 5.0, 7.0],
+        }
+    )
+    result = bioframe.assign_view(df, view_df, drop_unassigned=True)
+
+    # chr2:10-20 is outside the view and dropped; chr1:10-20 is assigned and kept
+    # even though its `value` is NaN.
+    assert list(zip(result["chrom"], result["start"])) == [("chr1", 10), ("chr1", 30)]
+    assert pd.isna(result.loc[0, "value"])