CHANGES IN VERSION 1.4.27
 -------------------------
    o Bioconductor minor build warning fix
    o Bug fix in somatic interactions plot. Issue: #135

CHANGES IN VERSION 1.4.26
 -------------------------
    o Bioconductor minor build warning fix

CHANGES IN VERSION 1.4.26
 -------------------------
    o Bioconductor minor build warning fix

CHANGES IN VERSION 1.4.25
 -------------------------
    o Fix messed up vignette for real
    o fix gistic plotting bug
    o bold font faces for plots
    o Corrects an issue wherein MAFtools accidentally renamed columns with names that contained a required column as a substring of their name. PR: #123

CHANGES IN VERSION 1.4.21
-------------------------
    o Fix messed up vignette

CHANGES IN VERSION 1.4.20
-------------------------
BUG FIXES
    o Bug fix in icgcSimpleMutationToMAF while converting ICGC maf to MAF object in. Issue: #105
    o Bug fix in oncomatrix function which earlier failed drop missing factors as well as resulted in error with zero samples. Issue: #96
    o Bug fix in mafCompare and forestPlot
    o Bug fix in mutSig file parsing. Issue: #120

IMPROVEMENTS
    o Add keepGeneOrder argument to coOncoplot. PR: #107
    o Changed order of plots in plotmafSummary for better visualization
    o Improved axis thickness and other plotting paramters for better pub-ready visualization

CHANGES IN VERSION 1.4.15
-------------------------
BUG FIXES
    o Set fixed seed value for extractSignature so that runs are reproducible. Issue: #101

CHANGES IN VERSION 1.4.10
-------------------------
BUG FIXES
    o Bug fix in read.maf which caused error when MAF contained single sample. Issue: #91
    o Bug fix in Oncoplot which caused plotting error while parsing mutsig results. Issue: #93
    o Enhancement to oncoplot. Added arguments annotationFontSize and annotationTitleFontSize to control annotations. Issue: #94

CHANGES IN VERSION 1.4.05
-------------------------
BUG FIXES
    o Bug fix in trinucleotideMatrix which caused error due to parsing of chromosome names in fasta file. Issue: #75
    o Bug fix in plotApobecDiff which messed up the order of genes in bottom bar plot. Issue: #80

CHANGES IN VERSION 1.4.00
-------------------------
NEW FUNCTIONS
    o plotApobecDiff - plots differences between APOBEC enriched and non APOBEC enriched samples
    o gisticOncoplot, gisticBubblePlot and gisticChromPlot to visualize GISTIC results
    o somaticInteractions - to identify mutually exclusive/co-occuring gene sets
    o genotypeMatrix - function to create genotype matrix
    o mutCountMatrix - generate count matrix

SIGNIFICANT USER-LEVEL IMPROVEMENT
    o Changes to MAF object: It now includes clinical data slot similar to PhenoData of expressionset objects.
    o Changes to MAF object: Silent variants will be stored seperately in MAF object and won't be mixed with non-syn variants.
    o Changes to MAF object: Oncomatrix is built on the fly whenever required, its no longer stored in MAF object.
    o You can specify a manual list of variant classifications to be considered as non-synonymous via argument vc_nonSyn in read.maf
    o Dropped mutExclusive function - Use somaticInteractions instead.
    o Many sorting options and plotting improvements to oncplots.
    o One can include q values from mutsig (or any similar program) as a side barplot in oncoplot
    o rainfallPlot can detect hyper mutated genomic segments via ChangePoint detection method
    o plotSignatures includes cosine similarity score and aetiology of detected signature
    o readGistic has argument cnLevel to choose deep or shallow CN variants
    o inferHeterogeneity includes MATH score in the plot
    o Tumor_Sample_Barcodes remains as is; earlier '-' were converted to '.' in sample names

NON SIGNIFICANT CHANGES
    o mafCompare output includes adjusted p-values
    o trinucleotideMatrix output includes adjusted p-values for APOBEC enrichment
    o added plot arguments to control title size and point size in lollipopPlot

BUG FIXES
    o Major bug fix in signature analysis
    o minor bug fixes in oncostrip