Update included references for hg38

[marchoeppner]

Hi,

this is probably a minor thing, but the documentation as well as the included references (accessibility etc) are very much focused around hg19. However, at this point we should probably consider hg19 defunct (or at least "bad practice"), given that hg38 came out 10 years ago. It would hence be nice if CNVkit could be updated throughout (incl. documentation) to use and refer to hg38/GRCh38.

/M

[serge2016]

# GRCh38.d1.vd1)
# https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files
refGenomeURL="https://api.gdc.cancer.gov/data/254f697d-310d-4d7d-a27b-27fbf767a834" # GRCh38.d1.vd1.fa.tar.gz
refGenomeFN0="GRCh38.d1.vd1.fa.tar.gz"
refGenomeFN="${refGenomeFN0%.tar.gz}"
refGenomeV="${refGenomeFN%.*}"

refGenomeFile="$REFDIR/$refGenomeV/$refGenomeFN"
refGenomeDir="$(dirname "$refGenomeFile")"
refGenomeFaiFile="${refGenomeFile}.fai"
refGenomeDictFile="${refGenomeFile%.*}.dict"

runDir="$(pwd)"
cnvkitRefDir="$runDir/$refGenomeV"
accessFile="$cnvkitRefDir/$GENOMEBUILD.bed"
mkdir -p "$runDir" "$cnvkitRefDir"

if [[ ! -s "$accessFile" ]]; then
    $CNVKIT access $refGenomeFile -o $accessFile
fi