How to use @single-cell-portal/igv - 4 common examples

}

  igv.createBrowser(igvContainer, igvOptions)

  // Log igv.js initialization in Google Analytics
  ga('send', 'event', 'igv', 'initialize')
  log('igv:initialize')
}


// Monkey patch getKnownGenome to remove baked-in genes track.
// We use a different gene annotation source, in a different track order,
// so removing this default gives our genome browser instance a more
// polished feel.
const originalGetKnownGenomes = igv.GenomeUtils.getKnownGenomes
igv.GenomeUtils.getKnownGenomes = function() {
  return originalGetKnownGenomes.apply(this).then(reference => {
    const newRef = {}
    newRef['GRCm38'] = reference['mm10'] // Fix name
    Object.keys(reference).forEach(key => {
      delete reference[key].tracks
      newRef[key] = reference[key]
    })
    return newRef
  })
}

igvOptions['search'] = searchOptions
  }

  igv.createBrowser(igvContainer, igvOptions)

  // Log igv.js initialization in Google Analytics
  ga('send', 'event', 'igv', 'initialize')
  log('igv:initialize')
}


// Monkey patch getKnownGenome to remove baked-in genes track.
// We use a different gene annotation source, in a different track order,
// so removing this default gives our genome browser instance a more
// polished feel.
const originalGetKnownGenomes = igv.GenomeUtils.getKnownGenomes
igv.GenomeUtils.getKnownGenomes = function() {
  return originalGetKnownGenomes.apply(this).then(reference => {
    const newRef = {}
    newRef['GRCm38'] = reference['mm10'] // Fix name
    Object.keys(reference).forEach(key => {
      delete reference[key].tracks
      newRef[key] = reference[key]
    })
    return newRef
  })
}

// that case.
    locus = [fallbackLocus]
  }

  const genesTrackName = `Genes | ${bamAndBaiFiles[0].genomeAnnotation.name}`
  const genesTrack = getGenesTrack(gtfFiles, genomeId, genesTrackName)
  const bamTracks = getBamTracks(bamAndBaiFiles)
  const tracks = [genesTrack].concat(bamTracks)

  const igvOptions = { reference, locus, tracks }

  if (typeof searchOptions !== 'undefined') {
    igvOptions['search'] = searchOptions
  }

  igv.createBrowser(igvContainer, igvOptions)

  // Log igv.js initialization in Google Analytics
  ga('send', 'event', 'igv', 'initialize')
  log('igv:initialize')
}

function initializeIgv(containerId, bamAndBaiFiles, gtfFiles, uniqueGenes) {
  // Bail if already displayed

  delete igv.browser

  const igvContainer = document.getElementById(containerId)
  igvContainer.innerHTML = ''

  const genomeId = bamAndBaiFiles[0].genomeAssembly

  let reference
  let searchOptions
  let fallbackLocus
  if (genomeId === 'Macaca_fascicularis_5.0') {
    fallbackLocus = 'chr1:1-2'

    // To consider:
    //  - Update genomes pipeline to make such files automatically reproducible
    const genomeAnnotationObj = bamAndBaiFiles[0].genomeAnnotation
    const genomePath =