Jordan Eizenga

Screen goes blank if you select a region starting at a node ID that does not have any threads associated with it

7

I think that's the explanation anyway. Literally everything disappears: the dropdown menus at the top, the actual visualization, the options menu at the bottom. Just a white Chrome window. It...

Visualization sometimes changes dramatically between starting the region from two adjacent nodes

1

Not quite sure how to fix this from an algorithmic point of view, but it's pretty confusing as a user. Here's an example, starting from node 1434110: ![screen shot 2019-02-27...

Choosing "Nodes" as the unit seems to still select a region in units of sequence length

1

For example, this does not look like 100 nodes: 

The problem seems to arise from not using `noexcept` in the constructors: https://stackoverflow.com/questions/8001823/how-to-enforce-move-semantics-when-a-vector-grows We may want to make this a requirement for the handle graph interface as well.

The ODGI graph does not pass the handle graph tests ported over from VG

9

I haven't looked into this deeply yet, but we should figure out whether this is the fault of the tests or the implementation, or perhaps a disagreement over the generality...

I made a mistake setting the resizing factor of the hash tables in PackedGraph, which it handled too gracefully for me to notice. I want to test out the fix's...

Pertains to https://github.com/edawson/gfakluge/issues/51 Here's a PR with the inline methods I talked about. I guess we also have some commits from Erik about memmapping in our master branch. I'll let...

Header only library fails linking if included in >= 2 object files

3

The gfakluge.hpp header consists mostly of methods that are neither inline nor template. That means it can't be included by multiple .cpp's, or else you will get redefinition errors at...

Fix compilation on centOS with gcc 11.2.0

1

I had to make some tweaks to get this to compile/run on my compute server: - Used `rm -f` instead of `-rm` so that `make` doesn't report itself as having...

I ran with this command: ``` python3 main.py --reads alpha_reads.fastq.gz -o verity_map_output_alpha -t 16 -d hifi-diploid assembly.haplotype1.fasta assembly.haplotype2.fasta ``` According to the `veritymap.log` the run completed successfully: ``` 02:09:13 59.8Gb...