Mitchell Robert Vollger
Mitchell Robert Vollger
Hi Heng, I am looking at a 1 Mbp region on chr16 that doesn't seem to align when comparing GRCh38 and T2T, but there is a lot of homology in...
Hi, This is basically a duplicate/reminder of https://github.com/lh3/minimap2/issues/491 but for `yak`. In short if `-K` is too large it only processes one sequence at a time. Will process many at...
Hello, I have found that if you merge a multitrack d4 file with additional files the resulting file will only include columns up through the first multitrack d4 file in...
Hello, I am running into a weird issue where if I include the "0" base of a chromosome in my view command I get a different result than if I...
Hi, It would be nice to further paralyze DupMasker. The step I find that takes a long line is the "Searching for duplicons..." step which looks like it is just...
Hi @38, Would you be able to cut a new release of d4tools, pyd4, etc? It would be great to have a release that included these fixes you worked on...
Hi @38 and @arq5x, I am getting an error when trying to open a d4 matrix in pyd4: ``` OSError: memory map must have a non-zero length ``` I have...
Hi Jason, With the release of networkx 2.4 the syntax ```G.node``` is removed in favor of ```G.nodes``` (https://networkx.github.io/documentation/stable/release/release_2.4.html), and running Peregrine with this version of networkx results in the following...
Hi, Is it possible to precompute the liftoff database from a gff without running the whole pipeline. The use case is that I have one reference and gff and I...
Hi @noamteyssier, Thanks so much for adding unionbedg for me! It has been really useful. However, I have found a corner case where the tool is not in sync with...