Groza Cristian

Calling large gaps in small contigs

2

Hi, I have somewhat short contigs in the range of 8 to 15 kbp. These contigs contain a 6 kbp insertion and are surrounded by 1 to 4 kbp of...

Hi, Could the Makefile for this project be modified to create a library file, similar to minimap2? I am trying to compile and link against minigraph. And could this be...

Fermi-lite aggressive trimming

1

Hi, When setting aggressive trimming in fermi-lite to pop bubbles in heterozygous regions, what is the strategy being employed. Is the longer path in the bubble being kept or the...

Calling SNPs with svim-asm?

1

Hi, I see that svim-asm does a genome to genome alignment to detect SV calls. Is there any reason it could not also list the substitutions in the output VCF...

undefined reference to `handlegraph::algorithms::dijkstra(handlegraph::HandleGraph const*, handlegraph::handle_t, std::function<bool (handlegraph::handle_t const&, unsigned long)>, bool)'

2

Hi, I am trying to use the dijkstra algorithm defined in `libhandlegraph` but getting a linker error. ```` undefined reference to `handlegraph::algorithms::dijkstra(handlegraph::HandleGraph const*, handlegraph::handle_t, std::function, bool)' ```` There are not...

Hi, In overlap.cpp, the OverlapProcess.h is included but I don't seem to find it in the source code. Do you know where I could find it?

Fixes `read_rm()` broken call to `str_trim()`.

abPOA prune graph

9

Hi, Is it possible to delete nodes from a graph, then remap reads to it? If so, could I have small snippet showing how? It's not clear to me which...

kage installation error

2

I install kage via `pip3` which works fine: ``` pip3 install kage-genotyper ``` However, when I try to run it I get: ``` cgroza@ubuntu:~$ kage Traceback (most recent call last):...