svaha2
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edawson
Linear-time, low-memory construction of variation graphs
Hello，when I use command： `svaha2 -r tgraph.fa -v tgraph.vcf > test.gfa` to generate GFA file,I failed with the error info： `FASTA index found for tgraph.fa Parsed fasta index with 1...
Because we use a reference genome for input, we can easily generate rGFA. This also gets around the many issues of representing paths in GFA 1 and GFA 2. We...
Long vcf lines (such as those with the SV sequence in the ref/alt fields) silently fail parsing. This is standard get_line behavior but is a major issue. Temporarily, I've fixed...
I have repeatedly run into this issue so it's high time I write it down. Variants in a vcf with adjacent positions will cause a segfault, probably because of some...
The GFA output of svaha2 is currently valid GFA 1. However, minigraph requires GFA overlaps in its output. This means the current output of svaha2 is invalid as minigraph input,...
This PR moves from GFA paths to the more stream-friendly Walk (W) line syntax. This should significantly reduce memory usage when outputting path information.