Jouni Siren

This is a known compiler bug. Apple Clang 13 crashes when compiling some vg sources on an M1 Mac running macOS Monterey. You may try reporting the issue to Apple,...

I'm not sure there is a fixed compiler. I get similar crashes when compiling GBWTGraph tests on my M1 laptop, so the crash is probably caused by libhandlegraph code.

After updating to macOS 12.3 and command line tools 13.3, everything seems to be working again.

The situation has not changed. Minigraph does not store enough information in the GFA to determine which paths in the graph correspond to the original assemblies. You have to align...

@glennhickey The path cover option exists, but it's not that suitable for real use. We got better results with 3 real samples in the HGSVC graph (which should be similar...

Do we want a general graph translation format that can handle alignments, different levels of detail, and so on? Or do we just need a way to state that segment...

There are two kinds of paths in VG: embedded paths (or just paths) that are stored in the graph itself, and lightweight paths (threads) stored in a GBWT index. Embedded...

The basic idea is this: ``` vg construct -r foo.fa -v foo.vcf.gz -a > foo.vg vg gbwt -v foo.vcf.gz -x foo.vg -g foo.gbz --gbz-format vg convert -Z -f foo.gbz >...

There is a data model mismatch between minigraph and vg. Minigraph outputs rGFA, which does not store the sequences as full-length paths. Instead, it annotates each segment (node) with information...

Let's see this line-by-line. The snakefile you followed was old, and many things have changed since then. ### Graph construction ``` vg construct -r {reference.fa} -v {vcf for SV} -a...