--sam-compact false is not working

[y9c]

Even --sam-compact false is set, the output is in compact mode rather than one alignment per line.

[y9c]

And it seem that gem3 failed to choose the best alignment as the primary alignment. As shown in this example output. Ref "U-25%-(V)" is be better than "U-0%-(V)" but this one is not assigned as primary.

test_read      0       U-0%-(V)        1       0       54M1S   *       0       0       GGGCACAAGACGACGCTAGGAAGCAACGAACGGGACCGGCCACGCGACGACGACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:10 MD:Z:12N0N0N0N1N0N0N0N5G1G25    AS:i:74 XA:Z:U-75%-(V),+1,54M1S,11;U-25%-(V),+1,54M1S,9;U
-25%-(D),+1,22M1I2M1D29M1S,11;U-50%-(V),+1,26M1I2M1D25M1S,11;