[Genome] maf2fasta

[Navin Elango]

Dear UCSC members,

I tried to use maf2fasta on a four species alignment and found the following
problem.

Lets say that the four species are A,B,C,D and the MAF file looks like the
following (I might be messing up the one-based or zero-based index, but the
point is that in the second block species C is missing)

a score=1234
s A 1 3 + 9 AAA
s B 1 3 + 9 AAA
s C 1 3 + 6 AAA
s D 1 3 + 9 AAA

a score=2345
s A 4 3 + 9 TTT
s B 4 3 + 9 TTT
s D 4 3 + 9 TTT

s A 7 3 + 9 GGG
s B 7 3 + 9 GGG
s C 7 3 + 6 GGG
s D 7 3 + 9 GGG

When I do maf2fasta, the output is

>A
AAATTTGGG
>B
AAATTTGGG
>C
AAATTTGGG
>D
AAA---GGG

The gap which is supposed to be in the third species is actually found in the
fourth species.

Am I missing something? Do I have to process the maf file before I send it
into maf2fasta? Could you please let me know how to fix this.

Any help will be greatly appreciated!

Thanks,
Navin.