Ghanshyam Chandra

Self-loop and cycles in rGFA

5

@lh3 In rGFA file (`test\MT.gfa`) there is a self loop, So can we expect graph generated with `minigraph -cxggs` or `minigraph --ggen` to contain self-loops or cycles?

conversion of GFA to rGFA

2

@lh3, I'm curious to know , whether we can convert `GFA` to `rGFA`? . As per [rGFA](https://github.com/lh3/gfatools/blob/master/doc/rGFA.md) format, we need to maintain 3 additional information along with each segment lines...

@lh3, Could you please explain what will be the `` required by `mgutils.js anno` for annotation of `rGFA` produced by `minigraph`?

Finding % mapped reads with GraphAligner

1

@maickrau As described in Table 1 of [GraphAligner](https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-020-02157-2.pdf), I want to calculate number of correctly aligned reads. In [GraphAligner](https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-020-02157-2.pdf), you have mentioned; "We consider a read correctly mapped if its...

@lh3, I was benchmarking the `radix_sort_128x()` function from minimap2 to perform anchor sorting (map.c [[Line 202](https://github.com/lh3/minimap2/blob/0cc3cdca27f050fb80a19c90d25ecc6ab0b0907b/map.c#L202), [Line 289](https://github.com/lh3/minimap2/blob/0cc3cdca27f050fb80a19c90d25ecc6ab0b0907b/map.c#L289)]). For small input sizes of anchors i.e. $\approx 10^5$, `radix_sort_128x()` produces stable...