gfatools
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lh3
Tools for manipulating sequence graphs in the GFA and rGFA formats
@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...
What is the format of the "A" line produced by `gfatools asm`? ``` S utg0000001l * LN:i:25977 RC:i:371 lc:i:25977 A utg0000001l 0 + 82117 0 401 A utg0000001l 16 -...
It seems that running `gfatools ed -c` produces invalid GAF as only 10 entries are present instead of 12 mandatory per spec E.g.: ``` NA21309#1 119129 0 119129 + >s60779>s60780>s60781>s60782>s60783s60785>s60786...
 how to convert the single path gfa from complex structures graph into fasta file with gfatools? thanks
Hello, I'm having trouble running `gfatools bubble` on a GFA file that has been processed with with `gfatools asm`. I'm working with a subgraph that I extracted from `minigraph` output...
Hello, I create a recipes for gfatools in bioconda bioconda/bioconda-recipes#26073 but gfatools actually didn't have license could you add one ? Thanks for your work.
Another discussion thread. It is probably too early to implement libraries now, but it would be good to start thinking about the topic. Currently, gfatools comes with [very preliminary APIs](https://github.com/lh3/gfatools/blob/master/gfa.h)...
Hello Heng, I'm getting myself familiar with the GAF format. One site of interest to me (an INS onto GRCh38), has several reads with the following column 6 (broken down...
I would like draw the assembly graph after having removed the alternative haplotype (extracted using purge_dups) from an assembly graph gfa file. Could you add a feature to gfatools blacklist...
Before using the command: `gfatools view -l 303726,303738 -r 20 Assembly-BothStrands.gfa > Assembly-BothStrands_303726-303738_r20.gfa` my GFA has the following elements: ``` S 5924062 GTTTCAAAAAAAAAAAAAGAGCATGGCTCTGG RC:i:400 L 5209751 + 5924062 + 18M1D6M...
