Clustering step excludes some windows (gda_clustering.py)

[aprimitiveone]

Thanks for the great tool!

It took me sometime, but now I know why some windows are missing from the cluster.bed (and related files in gda_out folder). In my case it were 233 out of about 5300 5kb windows present in the genome (non-model species, chromosome-level assembly). It seems like the windows that possess stretches of Ns are entirely excluded from the clustering and remain omitted also during the results file production. It would be better to incorporate them, maybe just in advance assigning them to the unclustered group (-1).

Cheers!