Create configuration for a JBrowse 2 text index

Source: R/text-index.R

Creates the necessary configuration string for an adapter to a text index for gene name search in the browser.

text_index(ix_uri, ixx_uri, meta_uri, assembly)

Arguments

ix_uri

the URI for the ix file

ixx_uri

the URI for the ixx file

meta_uri

the URI for the JSON metadata file

assembly

the assembly associated with the text index

Value

a character vector with the JSON text index adapter.

Details

Note: this function currently only supports aggregate indices.

For more information on JBrowse 2 text indices, visit: https://jbrowse.org/jb2/docs/config_guide/#text-searching

Examples

text_index(
"https://jbrowse.org/genomes/hg19/trix/hg19.ix",
"https://jbrowse.org/genomes/hg19/trix/hg19.ixx",
"https://jbrowse.org/genomes/hg19/trix/meta.json",
"hg19"
)
#> [1] "{\"type\": \"TrixTextSearchAdapter\", \"textSearchAdapterId\": \"hg19-index\", \"ixFilePath\": {\"uri\": \"https://jbrowse.org/genomes/hg19/trix/hg19.ix\", \"locationType\": \"UriLocation\"}, \"ixxFilePath\": {\"uri\": \"https://jbrowse.org/genomes/hg19/trix/hg19.ixx\", \"locationType\": \"UriLocation\"}, \"metaFilePath\": {\"uri\": \"https://jbrowse.org/genomes/hg19/trix/meta.json\", \"locationType\": \"UriLocation\"}, \"assemblyNames\": [\"hg19\"]}"