Brett Chapman

I've increased the swap space on my machine now, so there should be 2.2TB of available virtual memory. I'm trying to index again and see how it goes. I'm also...

Thanks @jeizenga for your input. I tried indexing the pruned graph but came up with an error: I first create an XG of the whole graph from each pruned packed...

Thanks @jeizenga Yes, my intent is to use ```vg giraffe``` for genomic read alignment and ```vg mpmap``` for RNA-seq read alignment. The main reason I'm now attempting the pruning approach...

@ekg @jltsiren @jeizenga I've tried ```odgi prune``` using these parameters: ```odgi prune -i barley_pangenome_graph_1H.og -o barley_pangenome_graph_1H.pruned.og -c 3 -C 345 -T``` Then converted to GFA, then PG: ``` odgi view...

Thanks @xchang1 I've been trying to install the 'for-brett' branch, but am struggling to get it installed. I've usually installed ```vg``` from docker. I first clone the branch, cd into...

```vg stats -R``` has finished running on the pruned XG graph. The largest snarl is 215479 in size.

Thanks @xchang1 I checked the docker repository but couldn't see the build there. Would it have the 'for-brett' tag? I also ran ```vg stats -R``` on the original non-pruned graph,...

Sure, I'll try and build from the Dockerfile again. I'll let you know how it goes.

The build failed: ``` /usr/bin/gcc -std=gnu11 -Wall -Wextra -Wsign-compare -Wundef -Wno-format-zero-length -Wpointer-arith -Wno-missing-braces -Wno-missing-field-initializers -pipe -g3 -fvisibility=hidden -Wimplicit-fallthrough -O3 -funroll-loops -I /vg/include -I /vg/include -c -D_GNU_SOURCE -D_REENTRANT -Iinclude -Iinclude -o...

Yeah, I clone the branch with ```--recursive``` I do the following: ``` git clone --recursive --branch for-brett https://github.com/vgteam/vg.git cd vg/ docker build -t local/vg . ```