Cytobands and chromosome alias

[dnil]

As always, thank you for a wonderful tool and all the good stuff!

We have an issue with the cytobands view. I imagine there are more pressing things, but maybe it is super easy to fix.

1kg hg19 cytobands

With IGV.js 3.2.0:

Maybe we need some additional alias configuration, or it is just a rare use case since we are mainly using 1kg_v37:

 reference: {
                        id: "hg19",
                        fastaURL: "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/1kg_v37/human_g1k_v37_decoy.fasta",
                        indexURL: "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/1kg_v37/human_g1k_v37_decoy.fasta.fai",
                        cytobandURL: "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/cytoBand.txt",
                        aliasURL: "https://igv.org/genomes/data/hg19/hg19_alias.tab"
                    },

✅ It can be seen in IGV.js v2.15.13:

❌ But appears to break in v3.0.0:

Perhaps the chromosome aliases are not fully taken into account for cytoband lookup? Thank you!

hg38 cytoBandIdeo.txt

On a sidenote, we saw some issues with the display from an old hg38 non-grayscale cytobands file (https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/cytoBandIdeo.txt) as well:

With IGV.js v3.2.0:

                reference:
                    {
                        id: "hg38",
                        fastaURL: "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa",
                        indexURL: "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",
                        aliasURL: "https://igv.org/genomes/data/hg38/hg38_alias.tab"
                    },

Whereas "https://igv-genepattern-org.s3.amazonaws.com/genomes/hg38/cytoBandIdeo.txt.gz" looks gorgeous:

With IGV.js v3.2.0:

    reference:
                    {
                        id: "hg38",
                        fastaURL: "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa",
                        indexURL: "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai",
                        cytobandURL: "https://igv-genepattern-org.s3.amazonaws.com/genomes/hg38/cytoBandIdeo.txt.gz",
                        aliasURL: "https://igv.org/genomes/data/hg38/hg38_alias.tab"
                    },

[dnil]

I just tested with a cytobandIdeo-file with chromosome names matched to the reference, which worked just fine. So from our horizon, feel free to call this a new feature. 😸 But maybe we could upload a matching file for the old 1kg_v37 for completeness.