Masked/Unmasked Beds

[nvlachos]

After experiencing an anomaly while trying to create a tree, i looked down into the code and files and discovered a possible bug. In my case, the reference file has a contig, actually 2, that gets masked starting at base 2. However, when trying to create the unmasked bed, the first region starts at 1 but does know how to set the stop point at base 1 also and leaves a null value as the stop for that region and causes issues downstream.

[lskatz]

That is troubling. Thank you for reporting it. I am using a new module in Lyve-SET v2 but I haven't run all the validation testing on it. There is a new perl module I am using for calculating ranges and maybe it fixes it? I will leave this issue open for when I can address it in the future.