hal2sg is producing a VariantSet for every genome in the HAL, but is only putting Alleles into VariantSet 0:
INSERT INTO VariantSet VALUES (0, 0, 'Anc0');
INSERT INTO VariantSet VALUES (1, 0, 'ref');
INSERT INTO VariantSet VALUES (2, 0, 'GI568335879');
INSERT INTO VariantSet VALUES (3, 0, 'GI568335954');
INSERT INTO VariantSet VALUES (4, 0, 'GI568335976');
INSERT INTO VariantSet VALUES (5, 0, 'GI568335986');
INSERT INTO VariantSet VALUES (6, 0, 'GI568335989');
INSERT INTO VariantSet VALUES (7, 0, 'GI568335992');
INSERT INTO VariantSet VALUES (8, 0, 'GI568335994');
INSERT INTO VariantSet VALUES (9, 0, 'GI568335997');
INSERT INTO Allele VALUES (0, 0, 'Anc0refChr0');
INSERT INTO Allele VALUES (1, 0, 'Anc0refChr1');
INSERT INTO Allele VALUES (2, 0, 'Anc0refChr2');
INSERT INTO Allele VALUES (3, 0, 'Anc0refChr3');
INSERT INTO Allele VALUES (4, 0, 'Anc0refChr4');
INSERT INTO Allele VALUES (5, 0, 'Anc0refChr5');
INSERT INTO Allele VALUES (6, 0, 'Anc0refChr6');
INSERT INTO Allele VALUES (7, 0, 'Anc0refChr7');
...
Instead, it should produce only one VariantSet.