fastloader

A JBrowse plugin to load BED tabix, VCF tabix, or BAM as a blank track if the index url gets a 404

Options

Three storeClass types are available

FastLoader/Store/SeqFeature/BAMLoader
FastLoader/Store/SeqFeature/VCFLoader
FastLoader/Store/SeqFeature/BEDLoader

Usage

You can set a urlTemplate to contain some variables, such as {refseq}, which can speed up loading for BAM or VCF files

The source code for src/JBrowse/Component.js describes default params

 * With no additional values given, knows how to interpolate
 * {refseq}, {refSeq}, {refSeqNum}, and {refSeqNumNoLeadingZeroes}.

So for example, you can use in your config file

urlTemplate=subdir/file.{refseq}.bam

And then have the BAM broken out by chromosome

subdir/file.chr1.bam
subdir/file.chr1.bam.bai
subdir/file.chr2.bam
subdir/file.chr2.bam.bai
...

Note that if you have a custom store you can add even more custom variables to interpolate

Example config

[tracks.MyTrack]
urlTemplate={refseq}.vcf.gz
storeClass=FastLoader/Store/SeqFeature/VCFLoader
type=CanvasVariants

Installation

Download the repo to plugins/FastLoader

Then add to the jbrowse config something like

"plugins": ["FastLoader"]