Tobias Rausch

bridge_lchains assertion error

1

Hi, With the [prebuilt GRCh38 pangenome graph](https://zenodo.org/record/6499594) I am getting an assertion error. `minigraph -t 1 -cx lr GRCh38-90c.r518.gfa.gz reads.fa` `minigraph: gchain1.c:391: bridge_lchains: Assertion `l0->v == l1->v' failed.` Below is...

conversion to stableGaf incorrectly assigns forward orientation

1

Hi Heng, Thanks for pointing out the stableGaf conversion script! When reverse orientation reads align to a single segment (stable sequence), such a GAF line is reduced to PAF (which...

Hi Heng, Extracting a chm13 subsequence and aligning it back to the pre-built graph results in an incorrect path alignment (deviating from rank 0 nodes) with lots of small InDels:...

Hi, Read bases before and after `query start` and `end` reported in minigraph mappings sometimes perfectly match the segment (S) sequence. Here is an example where I converted GAF ​​to...