Xian Chang

Distance index 2

4

## Changelog Entry To be copied to the [draft changelog](https://github.com/vgteam/vg/wiki/Draft-Changelog) by merger: * Update distance index 2 to be more efficient and make clustering faster * Minimizers now have a...

This is the same as #3736 but from vg's branch instead of mine, I just want to run all the tests and make a docker container

Update net_handle_t bindings to include equality and hash

1

I wanted `net_handle_t`'s to be used in sets in python so I needed the bindings to include equality and hashing. @adamnovak or maybe @ctcisar, can I do this? It looks...

Hi again, I got panaligner working with the [minigraph graph](https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/minigraph/hprc-v1.0-minigraph-chm13.gfa.gz) this time, but it is very slow now- it took about an hour to run 1,000 r10 reads on 8...

Low accuracy on simulated reads and overlapping primary alignments

3

Hello, I am trying to compare the performance of different mappers on long reads and minigraph has unexpectedly low accuracy. I'm mapping 1 million simulated HiFi and R10 reads to...

GraphAligner slow on R10 reads mapped to hprc graph

2

Hi @maickrau, I'm trying to map Nanopore R10 and Hifi reads to the HPRC graph and its super slow- I'm mapping 1 million reads on 64 threads and it still...

Python nethandles

2

This updates libhandlegraph to make equality of `net_handle_t`'s show up in the python bindings. Update of #190

Add a function to get the number of children of a snarl

Snarl child count

1

## Changelog Entry To be copied to the [draft changelog](https://github.com/vgteam/vg/wiki/Draft-Changelog) by merger: ## Description Add a unit test for new distance index function counting the number of children in a...

Distanceless distance indexing is very slow

1

I was trying to index a cabbage pangenome graph and it took ~25 days. The final distanceless distance index was 2.6 GB. There were 16,734,435 snarls, the largest has 227,992...