Changes in version 1.3.11 o When reducing overlapping reads, the read counts are now directly taken into account as weights for deriving the consensus sequence. To that aim, a custom function "weightedConsensusMatrix" is now used in place of "consensusMatrix" from Biostrings Changes in version 1.3.8 o Several minor changes including corrections to the documentation. For plotting the aligned reads, the user can now specify custom colours for certain types of annotated feature. See ?plotAligned for an example and details. Changes in version 1.3.6 o New function "countReadsAnnotated" to sum up aligned reads per category of genome feature (i.e. gene, ncRNA, etc.). o New function "medianByPosition" that allows for a memory-efficient computation of the median base quality at each nucleotide position in the reads Changes in version 1.3.5 o Changed implementation of 'sample' method. The 'Rle' objects used before were not suitable for large AlignedGenomeIntervals objects. 'sample' now uses the base::sample.int function. As a consequence only sampling with replacement is possible for the moment. o Added a logical argument 'both' to the 'fracOverlap' function. IF TRUE (default), both overlapping partners must be involved to at least a proportion of 'min.frac' in order to report the overlap; if FALSE, it suffices that one of the partners meets the 'min.frac' requirement. Changes in version 1.3.4 o Added an argument 'method' for the 'reduce' function. This argument supersedes the boolean argument 'exact', use 'method="exact"' in place of 'exact=TRUE'. Additional options are 'method="same5"' and 'method="same3"' to combine intervals that have the same 5' or 3'end, respectively. o Added a "fasta" format option to the export method for AlignedGenomeIntervals objects. Changes in version 1.3.2 o Added slot 'chrlengths' to S4 class 'AlignedGenomeIntervals' This optional slot stores a named integer vector of chromosome lengths. If present, it is used by 'coverage' and other methods, instead of obtaining those chromosome lengths from the annotation package indicated by the 'organism' slot. o Added an "export" method for objects of classes "Genome_intervals" and "Genome_intervals_stranded" Changes in version 1.1.15 o Certain functions (reduce, interval_overlap, fracOverlap) got an extra argument 'mem.friendly' that if set to TRUE (default: FALSE) leads to the data broken down into chromosome-wise batches for the computations, and thus for a "memory-friendlier", but slower, version of these computations. Changes in version 1.1.12 o Added a new function 'agiFromBam' which uses Rsamtools for creating AlignedGenomeIntervals objects directly from BAM files Changes in version 1.1.6 o Added an 'id' slot to AlignedGenomeIntervals objects, which allows users to assign a custom identifier to each interval Changes in version 1.1.5 o Added a 'sample' method for AlignedGenomeIntervals objects Consists of drawing a random sample of n of the aligned reads and returning the AlignedGenomeIntervals object defined by these aligned reads Changes in version 1.1.3 o Added a NEWS file o added a 'sort' method for AlignedGenomeIntervals to sort them by chromosome number > start position > end position o added a 'hist' method for AlignedGenomeIntervals which creates a histogram of the lengths of the reads aligned to the intervals Like the 'hist' function from package graphics, it returns an object of class 'histogram' and accepts the argument 'plot=FALSE' Changes in version 1.1.2 o in function 'fracoverlap', the argument 'min.frac' now applies to both intervals and specifies the minimum required fraction of each of the two interval widths by which two intervals should overlap in order to be marked as truly overlapping (before: only applied to the shorter of the two intervals)