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Changelog

Source: NEWS.md

SingleMoleculeGenomicsIO 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

SingleMoleculeGenomicsIO 0.1.4

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

SingleMoleculeGenomicsIO 0.1.3

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

SingleMoleculeGenomicsIO 0.1.2

  • Remove removeAllNAReads function (move to footprintR)

SingleMoleculeGenomicsIO 0.1.1

  • Add sampling mode to countStatePairs and countMismatchStatePairs

SingleMoleculeGenomicsIO 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.