(I am not part of the galaxy team)
On Oct 14, 2011, at 8:33 AM, Marcin Jakalski wrote:
The third issue is with the "Reverse Complement a MAF file"
tool. ... the coordinates change, meaning, tool starts counting
from the end position of a chromosome, not from the start
position. ... I think it would be better if the tool would keep the
I can't comment on your first two issues. But for the third one,
FWIW, keeping the original coordinates would produce a file that is no
longer correct according to the definition of the MAF format, which
can be found here:
So to do that I need to take the length of chromosome and subtract
the start position from it, then subtract length and only then I get
the same coordinate as in my set of intervals.
This is the reason why the MAF format carries the chromosome length on
Someone could make a tool that does it the way you suggest. Hopefully
they wouldn't call the result MAF.
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