NEWS

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SingleMoleculeGenomicsIO 0.1.9

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

SingleMoleculeGenomicsIO 0.1.8

• Add getBaseCoverageForBam and countAlignmentsInBam functions

SingleMoleculeGenomicsIO 0.1.7

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

SingleMoleculeGenomicsIO 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)

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.