[Genome] blat - stepSize vs. maxGap

[Isaac Ho]

Hi--

I wanted to clarify the definitions for a few of the terms in the Blat 
documentation.

What is the difference between stepSize and maxGap?   The explanation in 
the documentation that stepSize equals "spacing between tiles" is 
ambiguious to me. 

Also, which setting represents the variable "W" shown in Figure 1 of the 
BLAT paper published in Genome Research?  ( In that figure, W determines 
the maximum distance allowed between two tile hits s.t. they can be 
clumped together;  these tile hits must be located on the same diagonal, 
so no indels between them. )

Thanks,

Isaac