Version 1.3.3 ________________________________________________________________________________ - Use homegrown Rcpp based graph class and algorithm for clique extraction Version 1.1.12 ________________________________________________________________________________ - Bug fix: pangenome subsetting is now faster and actually correct Version 1.1.11 ________________________________________________________________________________ - Improvement: Various speed improvements - Fix namespace clash between Matrix and S4Vectors Version 1.1.10 ________________________________________________________________________________ - Feature: New class pgSlim for handling pangenomes with no ref to sequence data - Bug fix: safeAAread/safeDNAread would return wrong sequences when number of fasta files exceeded 2000 Version 1.1.9 ________________________________________________________________________________ - Feature: Threshold for core group classificaton can now be set (defaults to 1) - Improvement: Only investigate the neighbors to groups that have changed during iteration in neighborhoodMerge. Version 1.1.8 ________________________________________________________________________________ - Bug fix: Vignette error due to problems with reutils Version 1.1.7 ________________________________________________________________________________ - Feature: cdhitGrouping creates initial grouping based on cdhit algorithm - Feature: neighborhoodSplit now refines the splitting as a final step by merging highly similar groups sharing gene group up- or downstream - Feature: gpcGrouping can now precluster using CD-Hit - Feature: Key algorithms now reports progress and timing information - Feature: Custom linearKernel function that takes an upper similarity threshold to speed up comparisons. - Feature: Updated vignette, focusing on recommended workflow - Improvement: More performant pcGraph, neighborhoodSplit, pgMatrix methods - Improvement: pgMatrix now returns a sparseMatrix for lower memory footprint - Improvement: pangenome matrix no longer stored in pgInMem - Bug fix: Remove zerolength genes upon pangenome creation. - Bug fix: Batch accessing fasta files to avoid "too many open connections" error Version 1.1.6 ________________________________________________________________________________ - Skips some long running examples and tests to cut down on check time Version 1.1.5 ________________________________________________________________________________ - Bug fix: .fillDefaults now correctly extracts the frame in advance Version 1.1.4 ________________________________________________________________________________ - Fixing imports to import BiocGenerics, S4Vectors and IRanges in full Version 1.1.3 ________________________________________________________________________________ - Minor optimization of code - getRep now names genes by group name - transformSim now works on sparseMatrix rather than matrix objects - avoids coercing huge sparse matrices down to matrix format Version 1.1.1 ________________________________________________________________________________ - Fix bug that would affect pangenomes above 100 genomes when GPC was used with automatic tree creation. Version 1.1.0 ________________________________________________________________________________ - Added kmerSplit method Version 1.0.3 ________________________________________________________________________________ - Update to work with ggplot2 v2.0.0 - All imports from ggplot2, gtable and grid are now explicit Version 1.0.2 ________________________________________________________________________________ - Fixed bug in transformSim that would cause it to break on large similarity matrices - Fixed bug in orgTree only present with pangenomes over 100 genomes Version 0.99.0 ________________________________________________________________________________ - Submission to Bioconductor