SQLite 3.27

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CREATE TABLE dist(hexbin1 int, hexbin2 int, distance int, source int)
INSERT INTO dist(hexbin1, hexbin2, distance, source) VALUES
(1, 2, 10, 0), (1, 2, 10, 1), (1, 2, 12, 0), (1, 2, 100, 0),  
(3, 4, 20, 0), (3, 4, 20, 1), (3, 4, 22, 0), (3, 4, 200, 0);
DELETE FROM dist
WHERE rowid NOT IN (
  SELECT FIRST_VALUE(rowid) OVER (PARTITION BY hexbin1, hexbin2 ORDER BY distance, rowid) 
  FROM dist
)
SELECT * FROM dist


hexbin1
hexbin2
distance
source


1
2
10
0

3
4
20
0