Creates the necessary configuration string for an indexed BAM or CRAM alignment so that it can be used in a JBrowse custom linear genome view.

track_alignments(track_data, assembly)

Arguments

track_data

the URL to the BAM/CRAM alignments

assembly

the config string generated by assembly

Value

a character vector of stringified AlignmentTrack JSON configuration

Details

It is important to note that while only the BAM/CRAM file is passed as an argument, tracks_alignment assumes that a BAM/CRAM index of the same name is located with the file

For example:

track_alignments("data/alignments.bam")

Assumes that data/alignments.bam.bai also exists.

This is a JBrowse 2 convention, and the default naming output of samtools

For more information on creating an index with samtools, visit https://www.htslib.org/

Examples

assembly <- assembly("https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz", bgzip = TRUE) track_alignments("alignments.bam", assembly)
#> [1] "{\"type\": \"AlignmentsTrack\", \"name\": \"alignments\", \"assemblyNames\": [\"hg19\"], \"trackId\": \"hg19_alignments\", \"adapter\": { \"type\": \"BamAdapter\", \"bamLocation\": { \"uri\": \"alignments.bam\" }, \"index\": { \"location\": { \"uri\": \"alignments.bam.bai\" } } } }"
track_alignments("alignments.cram", assembly)
#> [1] "{\"type\": \"AlignmentsTrack\", \"name\": \"alignments\", \"assemblyNames\": [\"hg19\"], \"trackId\": \"hg19_alignments\", \"adapter\": { \"type\": \"CramAdapter\", \"cramLocation\": { \"uri\": \"alignments.cram\" }, \"craiLocation\": { \"uri\": \"alignments.cram.crai\" }, \"sequenceAdapter\": {\"type\":\"BgzipFastaAdapter\",\"fastaLocation\":{\"uri\":\"https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz\"},\"faiLocation\":{\"uri\":\"https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.fai\"},\"gziLocation\":{\"uri\":\"https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.gzi\"}} } }"