## ----setup, include = FALSE-------------------------------------------------------------------------------------------
options(width=120)
knitr::opts_chunk$set(
   collapse = TRUE,
   eval=interactive(),
   echo=TRUE,
   comment = "#>"
)

## ----eval=FALSE-------------------------------------------------------------------------------------------------------
# library(igvR)
# igv <- igvR()
# setBrowserWindowTitle(igv, "hg38 explicit")
# setCustomGenome(igv,
#                 id="hg38",
#                 genomeName="Human (GRCh38/hg38)",
#                 fastaURL="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa",
#                 fastaIndexURL="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai",
#                 cytobandURL="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/cytoBandIdeo.txt",
#                 chromosomeAliasURL=NA,
#                 geneAnnotationName="Refseq Genes",
#                 geneAnnotationURL="https://s3.amazonaws.com/igv.org.genomes/hg38/refGene.txt.gz",
#                 geneAnnotationTrackHeight=500,
#                 geneAnnotationTrackColor="darkBlue",
#                 initialLocus="chr5:88,621,308-89,001,037",
#                 visibilityWindow=5000000)
# 

## ----eval=FALSE-------------------------------------------------------------------------------------------------------
# 
# base.url <- "https://igv-data.systemsbiology.net/testFiles/sarsGenome"
# fasta.file <- sprintf("%s/%s", base.url,"Sars_cov_2.ASM985889v3.dna.toplevel.fa")
# fastaIndex.file <-  sprintf("%s/%s", base.url, "Sars_cov_2.ASM985889v3.dna.toplevel.fa.fai")
# annotation.file <-  sprintf("%s/%s", base.url, "Sars_cov_2.ASM985889v3.101.gff3")
# 
# Sys.sleep(2)
# 
# setCustomGenome(igv,
#                 id="Sars_cov_2",
#                 genomeName="Sars_cov_2.ASM985889v3",
#                 fastaURL=fasta.file,
#                 fastaIndexURL=fastaIndex.file,
#                 geneAnnotationURL=annotation.file,
#                 geneAnnotationName="ASM985889v3",
#                 geneAnnotationTrackHeight=500,
#                 geneAnnotationTrackColor="darkBlue",
#                 visibilityWindow=30000)
# 

## ----eval=TRUE--------------------------------------------------------------------------------------------------------
sessionInfo()