Comments (2)
We chose KFF because we wanted to avoid adding yet another major dependency. VG already has too many of them, making the build system fragile.
As for random access, we also need it in vg haplotypes
. We simply load the kmer counts into a hash map. On my laptop, that takes ~100 seconds for the counts from 30x reads: 25 seconds for prepopulating the hash map with the kmers we are interested in and 75 seconds for multithreaded reading.
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Understood. I agree about the dependencies!
I'll copy your comment on the similar issue I created at Pangenie (eblerjana/pangenie#62). Maybe you and Jana can help each other get behind one kmer ecosystem for pangenome analysis.
Best,
Joe
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Related Issues (20)
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