Merge branch 'master' of https://github.com/hartwigmedical/hmftools

orange/README.md

@@ -197,7 +197,7 @@ The chapter presents the following:
 
 In case ORANGE was run in DNA+RNA mode, the alleles will be annotated by RNA fragment support.
 
-- Genomic immune escape analysis (inspired by [this paper](https://www.biorxiv.org/content/10.1101/2022.02.23.481444v1.full.pdf)),
+- Genomic immune escape analysis (inspired by [this paper](https://www.nature.com/articles/s41588-023-01367-1)),
   with the following mechanism that ORANGE makes an attempt at detecting:
     - HLA-1 loss-of-function, detected in case one of the following mutations is present in either HLA-A, HLA-B or HLA-C:
         - MACN < 0.3 without the presence of a loss (proxy for LOH)