CHANGES IN VERSION 1.10.0
------------------------

    o Bug fixes and documentation improvements


CHANGES IN VERSION 1.8.0
------------------------

    o Bug fixes and other improvements


CHANGES IN VERSION 1.6.0
------------------------

    o New vignette

    o Changes in the SGVariants and SGVariantCounts class. Instances
      created with previous versions of SGSeq have to be updated. 

    o Replaced functions for accessing assay data with two generic functions
      counts() and FPKM()

    o Support BamFileLists in sample info

    o Changed behavior of the annotate() function when assigning gene names

    o Changed behavior of the min_denominator argument in
      analyzeVariants() and getSGVariantCounts(). The specfied minimum
      count now has to be achieved at either the start or end of the event.

    o Adjacent exons no longer cause a warning in convertToTxFeatures()

    o Deprecated legacy classes TxVariants, TxVariantCounts

    o Bug fixes and other improvements


CHANGES IN VERSION 1.4.0
------------------------

    o Added importTranscripts() for importing annotation from GFF format

    o Added plotCoverage() for visualization of per-base read coverage
      and junction read counts

    o Added predictVariantEffects() for predicting the effect of splice 
      variants on annotated protein-coding transcripts

    o findSGVariants() is now able to deal with more complex gene models

    o SGVariants columns closed5p and closed3p now refer to individual
      splice variants rather than the splice event they belong to

    o Bug fixes and other improvements


CHANGES IN VERSION 1.2.0
------------------------

    o Renamed class TxVariants to SGVariants

    o Renamed class TxVariantCounts to SGVariantCounts

    o Renamed findTxVariants() to findSGVariants()

    o Renamed getTxVariantCounts() to getSGVariantCounts()

    o Parallelization is now controlled with a single cores argument

    o Argument max_complexity for predictTxFeatures() controls 
      skipping of problematic regions

    o getBamInfo() is no longer run as part of analyzeFeatures()

    o getSGVariantCounts() now supports obtaining counts from BAM files

    o Bug fixes and other improvements
