Mosaik - Read Names Trimmed

[sichan]

Hello All,

I'm aligning SOLiD paired reads. The forward (F3) reads are 50 long, while the reverse (F5-P2) reads are 35 long. Can Mosaik handle paired reads of different lengths?

My paired read names look like this:
>4_37_1284_1
>4_37_1284_2

Afterwards, the read names have been trimmed:
>4_37_128
>4_37_128

Even after specifying excplicity for Mosaik to *not* trim the read names (-tpr 0 -tsr 0 within MosaikBuild), my read names are still trimmed. Has anyone encountered this before? Incidently, MosaikBuild does not like read names that look like this:
4_37_1284/1
4_37_1284/2

Thanks.