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smarco / gem3-mapper

GEM-Mapper v3
GNU General Public License v3.0
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--sam-compact false is not working #37

Open y9c opened 2 hours ago

y9c commented 2 hours ago

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

y9c commented 2 hours ago

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;