MutationalPatterns v1.1.3 (Release date: 2017-04-20)
=====================================================

Fourth preparation release for Bioconductor 3.5.

Bugfixes:
* Add missing package to 'Suggest' field.

MutationalPatterns v1.1.3 (Release date: 2017-04-20)
=====================================================

Third preparation release for Bioconductor 3.5.

Bugfixes:
* Fix running of a unit test.
* Fix another build problem for Windows.

MutationalPatterns v1.1.2 (Release date: 2017-04-18)
=====================================================

Third preparation release for Bioconductor 3.5.

Bugfixes:
* Properly read external data for tests.
* Fix build problems on Windows.


MutationalPatterns v1.1.1 (Release date: 2017-04-12)
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Second preparation release for Bioconductor 3.5.


MutationalPatterns v1.1.0 (Release date: 2017-04-06)
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Preparations for Bioconductor release 3.5.

Interface changes:
* 'read_vcfs_as_granges':  The 'genome' parameter
  must now be the name of a BSgenome library, to prevent
  problems with seqlevels style.

  The function now accepts an optional 'group' parameter to
  use a subset of chromosomes.

  It also accepts  the new optional 'check_alleles'
  parameter to significantly speed up the reading of VCF files.

* 'plot_contribution': This function now accepts an
  optional parameter 'palette' to specify custom colors.

Performance updates:
* Implement parallel execution in 'read_vcfs_as_granges',
  'mut_matrix' and 'mut_matrix_stranded'.

Bugfixes:
* Fix 'mut_type_occurences' to handle missing types.
* Fix 'mut_matrix' and 'mut_matrix_stranded' to emit warnings
  when processing empty GRanges.
* Fix inconsistencies in the README and the vignette.

Other changes:
* Various vignette updates.
* Added unit tests for 'read_vcfs_as_granges', 'mut_matrix',
  and 'mut_matrix_stranded'.


MutationalPatterns v1.0.0 (Release date: 2016-10-19)
=====================================================

Bioconductor release 3.4.


MutationalPatterns v0.99.6 (Release date: 2016-10-14)
=====================================================

Changes:

* Renamed functions: 'mut_type_occurences' to 'mut_type_occurrences',
    'strand_occurences' to 'strand_occurrences'.

MutationalPatterns v0.99.5 (Release date: 2016-10-06)
=====================================================

Changes:

* Added deprecation and defunct messages to functions that have
  changed since the v0.99.0.
* Various small vignette and reference manual updates.


MutationalPatterns v0.99.4 (Release date: 2016-10-05)
=====================================================

Changes:

* Internal package loading changes.
* Removed files that do not belong to the package.

MutationalPatterns v0.99.3 (Release date: 2016-09-28)
=====================================================

Changes:

* Renamed functions: 'get_mut_context' to 'mutation_context',
    'get_type_context' to 'type_context',
    'get_muts' to 'mutations_from_vcf',
    'get_strand' to 'strand_from_vcf'.
* Added an explanation for the difference between
    SomaticSignatures and MutationalPatterns in the vignette.


MutationalPatterns v0.99.2 (Release date: 2016-09-23)
=====================================================

Changes:

* Renamed functions: 'vcf_to_granges' to 'read_vcfs_as_granges',
    'get_types' to 'mutation_types'.


MutationalPatterns v0.99.1 (Release date: 2016-09-13)
=====================================================

Changes:

* Renamed functions: 'read_vcf' to 'vcf_to_granges'.
* Removed functions: 'bed_to_granges', 'estimate_rank', 'rename_chrom'.
* Parameter changes: 'plot_rainfall', 'vcf_to_granges'


MutationalPatterns v0.99.0 (Release date: 2016-09-12)
=====================================================

Changes:

* Package created