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GMOD / jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
http://jbrowse.org
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bgzf-tabix -> VCF binary data backend #211

Closed rbuels closed 11 years ago

rbuels commented 11 years ago

Read data directly from VCF files that are compressed and indexed with bgzf and tabix.

Probably try to make a generic store base class that handles bgzf/tabix data, and that can be inherited from.

rbuels commented 11 years ago

Should support same format as UCSC: http://genome.ucsc.edu/goldenPath/help/vcf.html

rbuels commented 11 years ago

Work is going on in the vcf branch

vsmalladi commented 11 years ago

Would adding in support for tabix VCF allow for bigBed file format as well?

rbuels commented 11 years ago

No, that's a separate format. Do you use bigBed? You are the first person I've heard from that seems interested in JBrowse bigBed support.

vsmalladi commented 11 years ago

I was more curious on support for local bed files, since now local BAM, bigWigs and GFF3 files were supported.

rbuels commented 11 years ago

Ah. Sure, local BED file support is worthwhile. Opened issue #218 for this.