Fix issue with combine operation merging seqnames (#130)

BiocPy · Oct 15, 2024 · 81c93e8 · 81c93e8
1 parent a22165f
commit 81c93e8
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Showing 2 changed files with 18 additions and 3 deletions.
diff --git a/src/genomicranges/GenomicRanges.py b/src/genomicranges/GenomicRanges.py
@@ -3120,7 +3120,7 @@ def subtract(
 def _fast_combine_GenomicRanges(*x: GenomicRanges) -> GenomicRanges:
     return GenomicRanges(
         ranges=ut.combine_sequences(*[y._ranges for y in x]),
-        seqnames=ut.combine_sequences(*[y._seqnames for y in x]),
+        seqnames=ut.combine_sequences(*[y.get_seqnames() for y in x]),
         strand=ut.combine_sequences(*[y._strand for y in x]),
         names=None,
         mcols=None,
@@ -3149,7 +3149,7 @@ def _combine_GenomicRanges(*x: GenomicRanges) -> GenomicRanges:
 
     return GenomicRanges(
         ranges=ut.combine_sequences(*[y._ranges for y in x]),
-        seqnames=ut.combine_sequences(*[y._seqnames for y in x]),
+        seqnames=ut.combine_sequences(*[y.get_seqnames() for y in x]),
         strand=ut.combine_sequences(*[y._strand for y in x]),
         names=all_names,
         mcols=ut.relaxed_combine_rows(*[y._mcols for y in x]),

diff --git a/tests/test_gr_methods_basic.py b/tests/test_gr_methods_basic.py
@@ -150,8 +150,23 @@ def test_combine():
     assert g_src is not None
     assert g_tgt is not None
 
-    out: GenomicRanges = ut.combine_sequences(g_src, g_tgt)
+    out = ut.combine_sequences(g_src, g_tgt)
 
     assert out is not None
     assert len(out) == 15
     assert len(out.get_mcols().get_column_names()) == 2
+
+
+def test_combine_diff():
+    a = GenomicRanges(["A"], IRanges([0], [10]))
+    b = GenomicRanges(["B"], IRanges([5], [15]))
+
+    assert a is not None
+    assert b is not None
+
+    out = ut.combine_sequences(a, b)
+
+    assert out is not None
+    assert len(out) == 2
+    assert len(out.get_mcols().get_column_names()) == 0
+    assert out.get_seqnames() == ["A", "B"]