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