Changes in version 0.1.9                        

  - Allow ignore.strand=FALSE in expandSEToBaseSpace
  - Add flank argument to expandSEToBaseSpace

                        Changes in version 0.1.8                        

  - Add getBaseCoverageForBam and countAlignmentsInBam functions

                        Changes in version 0.1.7                        

  - Default to sample reads from all chromosomes in the bam files if no
    explicit sequence name(s) are given

                        Changes in version 0.1.6                        

  - Fix reporting of total number of processed modifications
  - Avoid processing of prior modification data upon removing of
    soft-masked bases (may improve performance of readModBam
    several-fold)

                        Changes in version 0.1.5                        

  - Breaking change: Require specification of column names for read
    regrouping by to include the name of the nested colData column where
    they should be found
  - Do not allow column names in colData(se) containing ':'
  - Add addReadLevelAssay function to simplify addition of read-level
    assays to a SummarizedExperiment object
  - Add extractColDataColumns and getReadNamesBySample utility functions

                        Changes in version 0.1.4                        

  - Bug fix in padding of extracted sequence context for regions on the
    minus strand

                        Changes in version 0.1.3                        

  - Return bam header information in the metadata of results from
    readModBam, readMismatchBam, countStatePairs and
    countMismatchStatePairs

                        Changes in version 0.1.2                        

  - Remove removeAllNAReads function (move to footprintR)

                        Changes in version 0.1.1                        

  - Add sampling mode to countStatePairs and countMismatchStatePairs

                        Changes in version 0.1.0                        

  - Add readMismatchBam and countMismatchStatePairs supporting BAM files
    from Bisulfite-seq or deaminase-based experiments.
  - Initialize reading functions based on footprintR v0.4.0.