mSigSpectra 0.1.3

• Changes requested in the CRAN review of 0.1.2:
  • License field is now GPL-3 and the redundant LICENSE file has been removed.
  • Acronyms (VCF, SBS, DBS, ID, PDF) are spelled out in DESCRIPTION and software names are single-quoted.
  • Added \value sections to the documentation of check_and_remove_discarded_variants(), is_catalog(), and subset_catalog(), and to all internal helper documentation.
  • quick_check_vcf() no longer uses print() to format the multiple-ALT warning.

mSigSpectra 0.1.2

• Initial CRAN submission.
• Provides a four-step pipeline for building mutational-spectrum catalogs from VCF files: read_vcf(), split_vcf(), annotate_sbs_or_dbs_vcf() / annotate_id_vcf(), and vcf_to_sbs_catalog() / vcf_to_dbs_catalog() / vcf_to_id_catalog().
• Supports SBS, DBS, and indel (ID) catalogs for GRCh37, GRCh38, and GRCm38 reference genomes or any BSgenome genome. Adds transcript-strand annotation where transcript-ranges info is available.
• Ships example Strelka and Mutect VCFs in inst/extdata/ and a vignette demonstrating the full pipeline.