I am using GsnapParam to construct the parameter before using the gsnap function. I have the intron-level splicing in a file (L42.intron) that looks like:

>AF117653.intron1 AF117653:12113..12250
>AF117653.intron2 AF117653:12337..12704

I would like to detect splices from this file but don't how which argument I should use. In comment line, I use the -s flag (-s L42.intron). Which argument in the GsnapParam constructor is equivalent to the -s flag. Should I create a GmapSplice object and feed in to the 'splicing' argument? Help? 

Thanks,

Chao-Jen

Fred Hutchinson Cancer Research Center 
1100 Fairview Avenue N., M1-B514 
PO Box 19024 
Seattle, WA 98109 
206.667.4485 
cwon2@fredhutch.org