Hi All,
hts_idx_load_core seems to consume a significant amount of running time when
VCF files are queried on small regions. I have thousands of VCF files (more are
coming) with the file size of vcf.gz about 100 MB and vcf.gz.tbi about 1 MB. A
common use case is to query these VCF files on nearby small regions, for
example the CDS regions of a gene. I have C++ codes linked to htslib to run my
queries and I found that hts_idx_load_core takes a lot of running time because
hts_idx_load_core always loads the whole tbi even though the query regions are
on a single chromosome. I tinkered with hts_idx_load_core so that it loads only
the chromosome of interest instead of the whole tbi. And I can get VCF query
running 10 times faster.
I am wondering if this is the right approach to speed up VCF query. Any
suggestion is welcome. Thanks,
Yi-Shiou Chen
3DS.COM/BIOVIA<http://www.3ds.com/BIOVIA>
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