"ERROR: Unknown tag RG!" when processing alignments with 'XA' tag

[Christina-hshi]

Hello,

Thanks for developing this useful tool!
I run into the "ERROR: Unknown tag RG!". With some tests, I found that the error was triggered when handling an alignment record in a SAM file with an "XA" tag. See the example below.

GWNJ-1012:1036:GW2307303391th:4:1101:14308:32503        99      14      69934315        10      125S25M =       69934315        24      CGGTTTAGCACTGCCTGCAGCCCAGGGCATGATCCTGGAGACCTGGGATCGAGTCCCACGTCAGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTAACTGTGTCTCTGCCTCTCTGTCTCTAGCTGTGTCTCTATGAATAAATAAATAAAA     FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF     NM:i:1  MD:Z:24G0 MC:Z:48S24M78S   AS:i:24 XS:i:22 XA:Z:3,+109034706,127S22M1S,0;12,+32790526,127S22M1S,0;X,-23090765,1S22M127S,0;

I would appreciate it if you can look into this.

Thanks,
Christina