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Tabix gff #670
This pull request adds the ability to open GFFs that are Tabix indexed (yay)
I was able to test it out on some NCBI data for Apis mellifera, and I could use the indexed fasta and tabix GFF together for speedy loading.
I also adopted the existing GFF3 jasmine tests for GFF3Tabix just to ensure some testing on the new data source!
Users can open the Tabix GFF by selecting the bgzipped gff and the tbi file, similar to opening the VCF, and the track type will be recommended. Non-indexed GFF is still supported as well!
Also see #265
Thanks! I hadn't even realized that tabix did gff for awhile, but once I saw that it did on the command line, i got motivated to make this...
Also, I just remembered that it would be good to integrate tabix gff with generate-names.pl (tabix vcf is supported by generate-names) but I wouldn't consider that a showstopper...it's just way more efficient to use the tabix gff versus the unindexed one :)
Also, the best way to create the tabix gff is to first sort it and "tidy" it with http://github.com/genometools/genometools
Then bgzip/tabix workflow is standard!
This was referenced
Dec 16, 2015
Don't know if this is the right place to raise my question.
I just 'copied' a similar BEDTabix function for 6 column bed format (chr/start/end/name/score/strand), however, I still have one specific question regarding to my own need: I have some features associated with 'name' and I put them as headers in bed.gz (like ##name ). Since the name can appear for tens of thousands times at different locations, so I don't want to add an additional column. Is there a simple way to map features and name when dealing lines loaded for further Store feature preparation ?
BED file I used:
referenced this pull request
Dec 21, 2015
Added a couple things