Changelog

Source: NEWS.md

GenomicBreaks 0.14.7

• Correct a bug in load_genomic_breaks() where sequence lengths would be too long of 1 nucleotide when loaded from MAF files.

GenomicBreaks 0.14.6

• Experimental support for loading sequence information from FASTA files.

GenomicBreaks 0.14.5

• Support loading MAF files where alignment sign is on the query.
• Correct example data to make it really one-to-one.

GenomicBreaks 0.14.4

• Remove dependency on BOOST thanks to C++ code taken from LAST (M. Frith / GPLv3+).

GenomicBreaks 0.14.3

New functionalities

• New scaffoldByFlipAndMerge() and splitSeqLevel() functions for trivial scaffolding by hand.

GenomicBreaks 0.14.2

New functionalities

• New GBreaksToMatrix() function to apply image processing approaches on scrambling patterns.
• New keepLongestPair() function to focus on the longest sequence feature in each genome.
• New wholeGenomeClassification() function to classify isolated alignments, collinear alignments, bridge regions and breakpoint regions.

GenomicBreaks 0.14.1

Bug fixes

• Correct a 1-nt shift in minus-strand coordinates of the query genome of GBreaks objects loaded from MAF files. This shift could cause overlapping ranges that crashed the coalescing algorithm.
• bridgeRegions() now returns empty GBreaks objects if no bridge region was found. Closes issue #20.
• Allow makeOxfordPlots() to work on genomes larger than the maximum 32-bit integer. Closes issue #24.

New functionalities

• New flipInversions() function to remove detected inversions before searching for nested ones.
• New filterDoubleInversions() function for extracting double inversions.

GenomicBreaks 0.14.0

• The load_genomic_breaks() function gains support for files in the Multiple Alignment Format (MAF).

GenomicBreaks 0.13.1

New functionalities

• The makeOxfordPlots() function gains a col argument for choosing to color by strand or by score.

Bug fixes

• In makeOxfordPlots(), the sequence names are now centered on their region.

GenomicBreaks 0.13.0

Important bug fixes

• The flagColinearAlignments() and coalesce_contigs() functions were corrected so that strandless ranges are called colinear when they satisfy the conditions on any strand. Before, they would be treated like plus-strand ranges, causing failure to detect colinearity on the minus strand.

New functionalities

• New getSeq() method for GRanges and GBreaks objects that have proper seqinfo for an installed BSgenome package.
• New pairwiseAlignment() method for GRanges and GBreaks objects, that will call getSeq() automatically.
• New “mid” option to the direction argument of get_bps(), to output breakpoints at mid-distance between ranges.
• New bridgeRegions() function that maps unaligned regions of the target to the query genome when they are flanked by colinear regions.
• filterTranslocations() gains a remove flag and flagTranslocations gains a both flag.
• swap gains a sort flag, so that in interactive sessions, gb |> swap() |> sort(i=T) can be replaced by the shorter gb |> swap(s = T).

Backwards-incompatible changes

• The function bp_heatmap now expects to genome sequences to be reachable via BSgenome::getBSgenome.
• The function dist2next now operates on GRanges and GBreaks, and its main argument is renamed to x.

GenomicBreaks 0.12.2

New functionalities

• The function forceSeqLevels() now operates on both the target and the query ranges of GBreaks objects.
• New example data set: Neurospora crassa chromosome III aligned to its homologue in Podospora comata: chromosome 7.
• New strand_randomisation_index().
• makeOxfordPlots() includes strand information in the returned object.
• New type = 'none' option for makeOxfordPlots(), for better customisation.

GenomicBreaks 0.12.1

• The plotApairOfChrs() function now plots the name of the selected sequence levels instead of target and query. The labels can be overriden with the dna_seg_labels parameters. Closes issue #6.

GenomicBreaks 0.12.0

Backwards-incompatible changes

• Removed selChroms parameter in makeOxfordPlots().
• New defaults for makeOxfordPlots(): fixed-ratio line plot with round ends and size of 1. Axis labels are now “target” and “query” by default. In any case, Seqname is displayed instead of genome name if there is only one sequence in the ranges object.

New functionalities

• New function orderQuerySeqLevels() to better diagonalise dot plots.
• New diag parameter in makeOxfordPlots() to diagonalise the plots by re-ordering query sequence levels.
• New size parameter in makeOxfordPlots()
• New guessSeqLengths() and forceSeqLengths() functions to use as last ressort when sequence lengths are not known.

GenomicBreaks 0.11.0

Backwards-incompatible changes

• Remove project-specific load_one_to_ones function.

GenomicBreaks 0.10.0

Backwards-incompatible changes

• Removed flagInsersions, redundant with flagTranslocations() and buggy on minus strands.
• plotApairOfChrs() now plots coordinates and a scale bar by default.

New functionalities

• New flagPairs() function to exhaustively flag windows of 2 successive GBreaks entries.
• New gb2xlim() function to narrow focus on plots made with plotApairOfChrs().
• New makeOxfordPlots() function to create macrosynteny plots. Thanks to Aleksandra Bliznina.
• In mergeSeqLevels(), use maximal end value for each seqlevel if no if no seqlengths were provided.
• A new set of example 5-uplets, to illustrate double inversions.
• Flag double inversions with flagDoubleInversions() and flagAll(), test them with exampleDoubleInversion.

Bug fixes

• Add strand check on flagTranslocations() so that it does not return a false positive on exampleDoubleInversion.

GenomicBreaks 0.9.1

New functionalities

• flagAll() now ensures that flags do not collide, and reports translocations.

GenomicBreaks 0.9.0

New functionalities

• New functions flagTranslocations(), showTranslocations() a filterTranslocations().
• New filterColinearRegions() function.
• New cleanGaps() function that is guaranteed to return only the intervals between the input ranges.
• The GBreaks() constructor now accepts three new parameters, target, query and strand, to construct GBreaks objects directly from GRanges objects.
• New range() methods for GBreaks objects, that runs GRanges::range on each pair of target/query seqnames, ignoring strand information.
• New subsetByOverlaps() range that combines regions overlapping by their target or by their query ranges.

Bug fixes

• flagColinearAlignments() now handles properly strandless ranges. (Issue #1)
• swap() now returns proper GBreaks() objects.

GenomicBreaks 0.8.0

Backwards-incompatible changes

• Remove flagInterruptions, which was nonsense.

New functionalities

• New isSorted() method to properly test with ignore.strand set to TRUE.
• Default plotApairOfChrs() to the first sequence level of the GBreaks object.
• plotApairOfChrs() now renders regions as blocks and not arrows as the strand information is encoded in the color and shape of the comparison bands. It also plots in light blue the blocks that are not matched. Closes issues #3 and #5.
• Added example data, see ?StructuralVariants and `vignette(“Structural Variants”, package = “GenomicBreaks”) for details.

Bug fixes

• In flagInversions(), check if input was sorted. Closes Issue #2.
• flagLongShort() now handles the case where some annotations do not match.

GenomicBreaks 0.7.1

• Fix namespace and variable bugs that were preventing reverse() to run.

GenomicBreaks 0.7.0

• New mergeSeqLevels() function to concatenate sequence features, for instance before plotting.
• New reverse() method for GBreaks and GRanges objects.
• Really return a GBreaks object in coalesce_contigs().
• Pass extra arguments from plotApairOfChrs() to genoPlotR::plot_gene_map.

GenomicBreaks 0.6.0

• Add pairwise chromosome plot functions using the genoPlotR package, see in particular plotApairOfChrs().

GenomicBreaks 0.5.3

• pkgdown update.

GenomicBreaks 0.5.2

• Greatly speed up flagLongShort().

GenomicBreaks 0.5.1

• Correct a variable name bug in flagLongShort().
• Export the GBreaks() constructor.

GenomicBreaks 0.5.0

• Add a flagLongShort() function to transfer annotations about chromosome arms.

GenomicBreaks 0.4.0

• Use alignments of Saccharomyces paradoxus to S. cerevisiae as example data.
• Addition of a GOC() function to calculate Gene Order Conservation.

GenomicBreaks 0.3.0

• Added the leftInversionGaps() function.

GenomicBreaks 0.2.0

• Document the package with pkgdown.