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brentp / vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0973-5
MIT License
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-ends handling is messy #6

Closed brentp closed 9 years ago

brentp commented 9 years ago

the -ends AnnotateEnds function is a major source of pain and bugs. See #5.

there's not a great way to handle this. It could be that only annotations that are tabixed can be used for -ends annotations. So, it would annotate the main interval, then if -ends is requested, it does a tabix call (now in go, but still does some file-handle stuffs) and appends the relateds for each annotation file.

That is probably the only option because they won't be sorted by the CIPOS start so the sweep won't work anyway.

brentp commented 9 years ago

this is somewhat better now. and will be in 0.8 release