Changes in version 1.9.2 o Keep metadata columns in targets o Adds function for splitting insertion sequences Changes in version 1.7.12 o Change CrisprSe$insertion_sites "idxs" column to read indices for reads with multiple insertions Changes in version 1.7.10 o CrisprSet method setCigarLabels now allows renaming labels Changes in version 1.7.9 o Updates mergeCrisprSets in accordance with new order of counting operations Changes in version 1.7.7 o Adds min and max for guide bounding box in plot o Fixes bug in plotFreqHeatmap caused when using "group" with a single row count matrix Changes in version 1.7.5 o Update tests after changes to allele counting o Added create.plot argument for plotFreqHeatmap with signature CrisprSet. o Adds an option "style" to plotAlignments for colouring only mismatch nucleotides o Changes to narrowAlignments for PacBio cigar format o Bug fix in collapsePairs. Only occurred when running outside of readsToTarget. o Adds "alleles" accessor for relating variant labels to the truncated cigar strings o Return unmergeable alignments instead of raising an error o Minor code changes to make it easier to run a non-standard counting pipeline o Code from initialisers split into separate files for easier readability Changes in version 1.7.4 o Added create.plot argument for plotFreqHeatmap with signature CrisprSet. Changes in version 1.7.2 o Allowing plotting arbitrarily many subsets of aligned regions Changes in version 1.7.1 o Reorganising plotAlignments code for allowing plotting subsets of the aligned regions. o Minor change to transcript plot plotVariants to make background white not transparent. Changes in version 1.5.9 o More comprehensive input checking in readsToTarget, removed redundant checking from CrisprSet initializer. o Fix bug where sequences falsely called no variant if target is on the negative strand but positive strand reference given. o Changed default SNV calling to 6 bases downstream instead of 5 to cover PAM o Added tests for mismatched reference and target Changes in version 1.5.8 o Adds an option to filter variants by name when counting or plotting Changes in version 1.5.7 o Fixes major bug preventing filtering in plotFreqHeatmap o Fixes bug in mergeChimeras if no chimeras mergeable Changes in version 1.5.6 o Autogenerate bam index for readsToTarget option chimeras = "ignore" Changes in version 1.5.3 o plotAlignments now accepts the same filtering arguments as variantCounts Changes in version 1.5.1 o New argument alleles in plotAlignments and plotFreqHeatmap for selecting which alleles to display or specifiying a plotting order o Removed unnecessary fields from CrisprRun class o New accessor function alns to get alignments from a CrisprSet o Improvements to plotAlignments to avoid unnecessary symbols in legend o Fix to header of plotFreqHeatmap when using type = "proportions" and providing sample order o consensusSeqs now returns cigars as metadata by default o Started indenting with four spaces at the start Changes in version 1.3.7 o Updates to vignette o Fix bug removing variants by name in variantCounts o Fixed argument legend.symbol.size being ignored in plotAlignmenta,DNAString-method. Changes in version 1.3.6 o Fix in new function mergeChimeras when no chimeras present Changes in version 1.3.5 o New option "minoverlap" in readsToTarget allows reads that do not span the target region to be considered o plotAlignments now works with character as well as DNAString objects o Merging of long gaps mapped as chimeras now possible Changes in version 1.3.4 o New function refFromAlns infers the reference sequence from aligned reads o Fixed bug causing an empty plot when plotting a single alignment with a large deletion o Changed annotateGenePlot from panel.margin to panel.spacing in accordance with recent ggplot2 versions o Added "create.plot" argument to plotAlignments for signature CrisprSet to make plot customisation easier. o Fixed bug in argument names when all alignments are chimeric o CrisprRun name now defaults to the coordinates when no name is provided Changes in version 1.3.3 o Fixed bug causing incorrect x-axis position in plotAlignments when strand unspecified Changes in version 1.1.6 o plotAlignments can now mark codon boundaries if codon frame is specified. o Added citation Changes in version 1.1.5 o More flexible specification of strand with new readsToTarget parameter 'orientation' o Fixed warning caused by implicit embedding of S4 objects o Added tests for 'plotAlignments' and 'annotateGenePlot' o Minor speedup and internal restructuring of 'annotateGenePlot' o Added CRISPR biocView o Changed NEWS to rd format Changes in version 1.1.4 o Fixed a bug that prevented SNV settings being used in some circumstances Changes in version 1.1.2 o new function consensusSeqs returns the consensus sequences of the variant alleles