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

## ----loadLibraries, results='hide'------------------------------------------------------------------------------------
# library(igvR)

## ----init, results='hide'---------------------------------------------------------------------------------------------
# igv <- igvR()
# setBrowserWindowTitle(igv, "CRAM Demo")
# setGenome(igv, "hg19")

## ----remoteCram, results='hide'---------------------------------------------------------------------------------------
# # 1000 Genomes Phase 3 Exome alignment (hg19)
# cram.url <- "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/exome_alignment/HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.cram"
# index.url <- "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/exome_alignment/HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.cram.crai"
# 
# track <- CramTrack(trackName = "Remote CRAM (HG00096)",
#                    cramUrl = cram.url,
#                    indexUrl = index.url)
# 
# displayTrack(igv, track)
# 
# # Zoom into a region with known coverage (e.g., HLA-A)
# showGenomicRegion(igv, "chr6:29,909,000-29,915,000")

## ----localCram, eval=FALSE--------------------------------------------------------------------------------------------
# # Assuming you started the server in the directory containing 'my_sample.cram'
# local.cram.url <- "http://localhost:8000/my_sample.cram"
# local.index.url <- "http://localhost:8000/my_sample.cram.crai"
# 
# track <- CramTrack(trackName = "Local CRAM (via localhost)",
#                    cramUrl = local.cram.url,
#                    indexUrl = local.index.url)
# 
# displayTrack(igv, track)

## ----sessionInfo------------------------------------------------------------------------------------------------------
# sessionInfo()