From 1c46f1e7c4acaf0ffbae4d851811b0e99e51ebc0 Mon Sep 17 00:00:00 2001
From: tony-kuo <tony.cy.kuo@gmail.com>
Date: Thu, 12 Sep 2024 10:21:14 -0700
Subject: [PATCH] enforce column vector in consolidate

---
 src/scimilarity/utils.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/scimilarity/utils.py b/src/scimilarity/utils.py
index dbd1887..51b959a 100644
--- a/src/scimilarity/utils.py
+++ b/src/scimilarity/utils.py
@@ -221,7 +221,9 @@ def consolidate_duplicate_symbols(
     dup_genes_data = []
     for k in dup_genes:
         idx = [i for i, x in enumerate(adata.var.index.values) if x == k]
-        counts = csr_matrix(adata.layers["counts"][:, idx].sum(axis=1))
+        counts = csr_matrix(
+            np.array(adata.layers["counts"][:, idx].sum(axis=1)).flatten()[:, None]
+        )
         gene_data = anndata.AnnData(
             X=csr_matrix(counts.shape),
             var=pd.DataFrame(index=[k]),