How to handle the gaps in the maf comparison block？

[helloworldABCD1234]

How to handle the gaps in the maf comparison block, such as
a
s chr1 ttgt-------TATAGCG
s chr2 TTgt------TAGTGAT
s chr3 tTgt------TAGTGAT
Can I delete the gap? Will this damage the integrity of the maf file？

[glennhickey]

As long as you only delete columns entirely of - characters, you won't affect the MAFs integrity (but there should be no such columns in the output). If you delete non-gap characters, then the coordinates become invalid. If you want a MAF with no gaps, you can try --maximumGapLength 0 or --raw to turn off block merging (you get get many more blocks though).