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Split VCF adapter #4853

Merged
merged 1 commit into from
Feb 20, 2025
Merged

Split VCF adapter #4853

merged 1 commit into from
Feb 20, 2025

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cmdcolin
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There are several VCF resources that split their files by chromosome name. Examples include 1000 genomes (https://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20130502/), 1000 bulls (https://www.ebi.ac.uk/ena/browser/view/PRJEB42783)

Not sure exactly why people do this, but such as it is, this PR adds an adapter that can read these split VCF files

You create a config like this

vcfGzLocationMap:{
  chr1: {uri:'...path to chr1 vcf'},
  chr2: {uri:'...path to chr2 vcf'}
}

you can optionally create an indexLocationMap too

the alternative method instead of a fully specified map would be to use "replacement strings" which jbrowse 1 allowed. could potentially allow both but this just does map for now

@cmdcolin cmdcolin merged commit b362a9f into main Feb 20, 2025
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@cmdcolin cmdcolin deleted the split-vcf branch February 20, 2025 03:22
@cmdcolin cmdcolin added the enhancement New feature or request label Feb 20, 2025
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