csi support
this release adds support for CSI. this can greatly speed up dense files like CADD and even gnomAD or ExAC.
to use, simply index your file with tabix as, e.g.:
tabix -m 12 --csi $file
and vcfanno
will prefer the .csi index over the .tbi.
refer to the performance page for how to optimize.
in brief, setting
export IRELATE_MAX_GAP=1000
seems to give good results. Please experiment and let me know what works for you. I can get ~60% speed improvement using csi'd ExAC to annotate clinvar with the above changes.