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