Adding Tumor-only mode for HTS (WGS) data

[jdemeul]

Implemented a minimally invasive approach for processing Tumor-only HTS (WGS) data with the latest ASCAT version. Highlights are as follows:

• ascat.prepareHTS will now run in tumor-only mode (and print this to the user) when no normal bam is provided.
• alleleCount is run on tumor only (duh) and the same counts are internally assigned to the normal, but not used or written to disk
• ascat.getBAFsAndLogR now has a tumor_only_mode=F default argument which gets set within ascat.prepareHTS
• Tumour LogR is calculated as log2(Tumour_Counts / mean(Tumour_Counts))
• Germline genotypes are inferred using ascat.predictGermlineGenotypes which has a new preset HTS_WGS_1000G which was tuned on in-house WGS data using the 1000G hg38 panel of loci provided with ASCAT.
• Main Documentation and Examples have been added

[bounlu]

Thanks for providing the tumor-only code for HTS. Will this also work for targeted seq? If not, is there a plan to integrate tumor-only mode for targeted seq?