elsiklab/fastloader

A JBrowse plugin for working with variable template parameters in BAM, VCF, tabix (the broken up index is "faster", hence fastloader)

fastloader's Issues

Idea: use BAI index

Could be an alternative to manually breaking up the BAM files https://github.com/hammerlab/bai-indexer

What's the advantage of loading this plugin

Even if I don't use this plugin, I can still broken up the bam files manually and then config as:

"storeClass" : "JBrowse/Store/SeqFeature/BAM",
"urlTemplate" : "dir/ICR.contig.{refseq}.bam",
"type" : "JBrowse/View/Track/Alignments2",

This also works. Then what's the advantage of loading this plugin?

How to set color according to SNP effect

I have got the SNP annotation using snpEff. I want to set color according to SNP effect.But I don't know how to set.
This is my setting
{ "storeClass" : "JBrowse/Store/SeqFeature/VCFTabix", "urlTemplate" : "tracks/marker/90k_snp.eff.vcf.gz", "tbiUrlTemplate":"tracks/marker/90k_snp.eff.vcf.gz.tbi", "label" : "wheat_90K", "category" : "Marker", "type" : "JBrowse/View/Track/CanvasVariants", "key" : "wheat_90K" },
I have added the FastLoader to my plugins files. But I don't know how to make it work，can you help me?
The below website is what I want. The snp have colored according its effect.
https://dubcovskylab.ucdavis.edu/jbrowse/?data=data%2Fjson%2Fiwgsc-2BS&loc=IWGSC_CSS_2BS_scaff_1562879%3A1..3416&tracks=tgacannot%2Cmipsannot%2CsnpsgenomeHC%2CcadsnpsHC%2Cmulticontigs%2Ccadmulticontigs%2Cblast%2CDNA&highlight=IWGSC_CSS_2BS_scaff_1562879%3A1..960&addFeatures=%5B%7B%22seq_id%22%3A%22IWGSC_CSS_2BS_scaff_1562879%22%2C%20%22start%22%3A%201%2C%20%22end%22%3A%20960%2C%20%22name%22%3A%20%22MyBLASTHit_1%22%2C%20%22description%22%20%3A%20%22evalue%200.0%22%7D%5D&addTracks=%5B%7B%22label%22%3A%22blast%22%2C%22store%22%3A%22url%22%2C%22type%22%3A%22JBrowse%2FView%2FTrack%2FHTMLFeatures%22%2C%20%22key%22%3A%22BlastHSP%20Results%22%7D%5D%0A