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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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Possible 4x speed up of merge --gvcf ref.fa #2106

Open pd3 opened 7 months ago

pd3 commented 7 months ago

This needs to be tested, but it appears that merge --gvcf ref.fa is 4x slower than merge --gvcf -. This may be caused by inefficient use of faidx_fetch_seq; would pre-loading and caching the reference sequence help?

jkbonfield commented 7 months ago

Have you tried doing a small file and using perf record (and perf report) to profile it? It'll soon point out where the differences in CPU lie.