[BioC] error with pileup function in ShortRead

[Davide Cittaro]

Hi, I'm trying to build a pileup vector from eland results.

p<-pileup(position(foo), 185, chromLen[chrom], svector, width(foo))

where foo is my AlignData class (filtered on chrom). It happens that I  
have a read on the + strand near the end of the chromosome (156 bp  
afar) that is greater than the specified fragment size (185). pileup  
complains that the chromosome length is too small... I can try to run  
with a shorter fragment size, but is there a way to tell pileup that  
the rightmost read can be smaller than the specified average size?

thanks

d

Davide Cittaro
davide.cittaro at ifom-ieo-campus.it