Hello Eric and Happy New Year! I hope you had a good holiday.
I encountered a potential bug related to split-sequences.
As per the segway docs,
> The --split-sequences=size option will split up sequences into windows with size frames each. The default size is 2,000,000.
However, this has not been my experience with Segway.
This is the command I used, note that I am working with a 10kb resolution.
segway train-init --resolution=10000 --num-labels=8 --num-instances=10 --segtransition-weight-scale=12.0 --include-coords=eval/include_coords.bed eval/GM12878/GM12878.genomedata GM12878_test/train
The max number of frames in my include_coords.txt file is 11559. This should be okay, since it is lower than the default size of 2,000,000.
awk '{print ($3 - $2)/10000}' include_coords.txt | sort -gr | head
11559
10446
9091
8828
8421
7942
7741
7522
7152
6846