rmTrans option

[nwales]

I'm quite interested in using the remove transitions option mentioned in the options list, but I cannot seem to get it to work. I tried various configurations, e.g. :

./ngsrelate extract_freq .mafs.gz .pos.glf.gz -rmTrans
./ngsrelate extract_freq .mafs.gz .pos.glf.gz -rmTrans 1
./ngsrelate -f .freq -g .pos.glf.gz -rmTrans
./ngsrelate -f .freq -g .pos.glf.gz -rmTrans 1

However, they all appear give the same results as without -rmTran (e.g. identical number of sites per pairwise comparison and essentially identical values for metrics). Have I missed something? I can rerun ANGSD with -rmTrans, but it would be quite handy to include this option for ease.

Cheers,
Nathan

[KHanghoj]

will have a look. thanks for info :)