Changes in version 1.1.0                        

  - To simplify the workflow, the gender of the patient is not taken
    into account anymore. That implies that in a male sample, a gain
    of 3 extra copies on the X or Y chromosome is considered as a gain
    and not an amplification anymore. For female samples, nothing
    changes.
  - The oncoscan coverage has been corrected to reflect only areas where
    there are groups of probes. Isolated probes where causing issues to
    identify arm-level alterations as ChAS segments where never extended
    to these probes and the 90% threshold could never be met
    (particularly on chromosomal arms 9p and Yq).
  - Minor corrections in vignette

                        Changes in version 1.0.0                        

  - The nLST test has been clinically validated on 384 patients from the
    PAOLA-1 trial and the recommended threshold is now >=15.
  - The default value for arm-level alterations has been set to 90% as
    mentioned in the publication [Christinat et al., J Mol Diagn 2021;
    PMID: 34454110].
  - The genomic LOH score (percent of LOH bases) has been added;
    score_gloh.
  - Adds a flag "no tumor?" if the percentage of altered bases is less
    than 1%.
  - Package to be released on Bioconductor

                        Changes in version 0.2.0                        

  - Novel HRD score (nLST: number of LSTs, normalized by ploidy):
    score_nlst
  - Change in Oncoscan workflow to use the nLST score and thresholds.
  - New function to compute the number of Mb altered (with or without
    LOH): score_mbalt
  - New function to compute the average copy number: score_avgcn
  - New function to estimate the number of whole-genome duplication
    events (based on the average copy number and the thresholds defined
    by Carter et al.): score_estwgd