Update igv.js chrom alias files to include alias for chrom M (Clinica…

…l-Genomics#4871)

Co-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>

CHANGELOG.md

@@ -18,6 +18,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - IGV.js WTS loci default to zoom to a region around a variant instead of whole gene
 - Refactored logging module
 - Case general report no longer shows ORPHA inheritance models. OMIM models are shown colored.
+- Chromosome alias tab files used in the igv.js browser, which now contain the alias for chromosome "M"
 ### Fixed
 - Broken heading anchors in the documentation (`admin-guide/login-system.md` and `admin-guide/setup-scout.md` files)
 - Avoid open login redirect attacks by always redirecting to cases page upon user login

scout/constants/igv_tracks.py

@@ -4,11 +4,11 @@
 )
 HG19REF_INDEX_URL = "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/1kg_v37/human_g1k_v37_decoy.fasta.fai"
 HG19CYTOBAND_URL = "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/cytoBand.txt"
-HG19ALIAS_URL = "https://s3.amazonaws.com/igv.org.genomes/hg19/hg19_alias.tab"
+HG19ALIAS_URL = "https://igv.org/genomes/data/hg19/hg19_alias.tab"
 
 HG38REF_URL = "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa"
 HG38REF_INDEX_URL = "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai"
-HG38ALIAS_URL = "https://s3.amazonaws.com/igv.org.genomes/hg38/hg38_alias.tab"
+HG38ALIAS_URL = "https://igv.org/genomes/data/hg38/hg38_alias.tab"
 HG38CYTOBAND_URL = (
     "https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/cytoBandIdeo.txt"
 )