(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 original coordinates.
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: http://genome.ucsc.edu/FAQ/FAQformat#format5
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 every line.
Someone could make a tool that does it the way you suggest. Hopefully they wouldn't call the result MAF.
Bob H