Changes in version 1.3.0 (2018-07-26)
+ Submitted to Bioconductor

Changes in version 1.3.1 (2018-08-15)
+ Updated DESCRIPTION file
  o replaced Author and Maintainer by Authors@R
  o added URL for BugReports
+ Changed from manual NAMESPACE and *Rd files to a creation by roxygen2
+ Changed function names for reading data from "load..." to "read..."
+ Shortened the longest function names
  o getGenomesFromMutationFeatureData -> getGenomesFromMutFeatData
  o getSignatureListFromEstimatedParameters -> getSignaturesFromEstParam
+ Used robust sequence creation with seq, seq_len, seq_along instead of 1:N etc
+ Consistent use of native class checking such as is.numeric()
+ Implemented wrapper functions for external classes which do not provide
  the necessary accessor functions
+ Replaced instances of sapply() and unlist(lapply()) by vapply()
+ Updated vignette and made most code chunks runnable
+ Added greedy search option to plotExplainedVariance (significant speed-up)

Changes in version 1.3.2 (2018-08-29)
+ Fixed a minor bug in mapSignatureSets() that occurred when the two signature
  sets had the same size.
+ Added functions to verify the format of signatures, genomes and exposures:
  o isAlexandrovSet(), isShiraishiSet(), isSignatureSet()
  o sameSignatureFormat()
  o isExposureSet()
+ Moved description of deprecated BiocInstaller in vignette to BiocManager.

Changes in version 1.3.3 (2018-09-24)
+ Implemented own signature plotting to remove code dependency from pmsignature
+ Decoupled the following data conversions functions from pmsignature code:
  o getGenomesFromMutFeatData()
  o getSignaturesFromEstParam()
+ Moved some common code to a new internal function for ease of maintenance.
+ Fixed bugs:
  o Error when some sequence names where not found in the reference genome,
    e.g., due to different names of decoy sequences.
  o Minor problems with unlikely signatures composed of only the mutated base
    (no flanking bases)

Changes in version 1.99.0 (2018-11-10)
+ When transcription direction is taken into account: exclude mutations in
  regions with overlapping genes of opposing transcription directions by
  default! Previous versions of decompTumor2Sig took the approach of
  pmsignature, using the transcription direction of the first gene encountered
  in the transcript database (which is rather arbitrary); excluding these
  mutations appears more appropriate. The old approach can still be used with
  an additional function parameter.
+ Removed pmsignature from the suggested packages (not allowed in Bioconductor)
+ Reduced the number of tumor genome examples in extdata for faster processing
  and smaller package size (six out of 21 tumors from PMID:22608084)

Changes in version 1.99.1 (2019-04-07)
+ Changed the procedure which converts lists of individual mutations from MPF
  files into tumor mutation profiles to reduce the memory footprint and
  allow for larger sets of tumors to be read from file.
+ When genomes are read from files: remove genomes without SNVs (no mutation
  frequencies)
+ Recognize indels for which either the REF or ALT base is specified as "-"
+ Fix bugs:
  o Error when quadprog returned a mutation frequency of minimally larger
    than 1 (which is theoretically impossible but can probably happen due
    to the rounding of floating point numbers)

Changes in version 2.1.0 (2019-08-18)
+ adapted readAlexandrovSignatures to read the file format used by the
  COSMIC mutational signatures version 3 (May 2019; Single Base Substitution/SBS
  signatures only)

Changes in version 2.4.1 (2020-07-27)
+ Removed dependency of package CRAN vcfR (archived on 2020-07-05), using
  functions of Bioconductor package VariantAnnotation instead
+ Improved the mutation filtering so that multiallelic SNVs aren't excluded
  when loading tumor genomes from a VCF file
+ Updated citation and affiliation information
+ Added consistency check for reference genome and genome annotation
+ Improved error messages

Changes in version 2.7.1 (2021-03-21)
+ Updated readAlexandrovSignatures() to add the possibility to read COSMIC
  signatures of version 3.1 directly from an Excel file (as provided on the
  COSMIC website).
+ Added possibility to adjust/normalize mutational signatures to specific
  subsets of the human genome (defined by means of GRanges objects). The
  adjustment/normalization is performed accoring to the nucleotide frequencies
  in the specified regions (with respect to nucleotide frequncies in
  the reference sequences, e.g., the whole genome, for which the signatures
  were derived in the first place).

Changes in version 2.7.2 (2021-03-26)
+ Updated readAlexandrovSignatures() to read the COMSIC signature format v3.2
  (published in March 2021).

Changes in version 2.7.3 (2021-04-01)
+ Fix: changed example for adjustSignaturesForRegionSet() to limit memory usage
  (previous example produced error during check on Windows for arch 'i386').
+ Fix: made sure that the extension of genomic regions by half the sequence
  pattern (needed for the adjustSignaturesForRegionSet() function) does not
  result in out-of-bounds regions.

Changes in version 2.13.1 (2022-05-09)
+ Fix: corrected recognition of EstimatedParameters (from package pmsignature)
  objects obtained with the use of a background signature.
+ Fix: corrected internal scripts for production of external example data.

Changes in version 2.23.1 (2024-11-21)
+ added an optional parameter ignoreRefMismatches to simply skip SNVs whose
  mutated REF base does not match the corresponding base from the reference
  genome (default is FALSE; should be used with care!)

Changes in version 2.99.0 (2026-07-07)
+ IMPORTANT: major version due to a change of the following default parameters:
  1) The default input signatures for readAlexandrovSignatures() have been
  removed. The previous default input (URL for COSMIC singatures v2) is not
  available anymore (fix was needed). Moreover, version 2 is outdated and
  it is preferable to not have any default input rather than another version
  that will sooner or later be outdated, too.
  2) The default reference genome and gene annotations, used for several
  functions, have been updated from human genome hg19 to hg38.
+ Additional features: the functions readAlexandrovSignatures(),
  readGenomesFromVCF() and readGenomesFromMPF() can now also take already
  loaded objects as input (VariantAnnotation::VCF or matrix representations of
  signatures or MPF data, respectively), rather than only file names or URLs
  from which to read the input.
+ The provided example VCF and MPF file have been reduced from six example
  genomes to three example genomes to reduce the package size and the
  package compilation time. For the latter purpose, also a workflow example
  in the vignette has been reworked to speed up its computation.
