在减少重叠读取时，读取计数现在直接作为派生一致序列的权重考虑。为此，一个自定义函数“weightedConsensusMatrix”现在被用于取代“consensusMatrix”，从Biostrings Changes版本1.3.8 o一些小的变化，包括对文档的更正。为了绘制对齐的读取，用户现在可以为某些类型的注释特征指定自定义颜色。看plotalign的例子和细节。新增函数“countReadsAnnotated”，用于汇总每一类基因组特征(即基因，ncRNA等)的对齐读数。o新的函数“medianByPosition”，允许在读取中每个核苷酸位置的中位碱基质量的内存高效计算。以前使用的'Rle'对象不适合大型的aligned genomeinterval对象。'sample'现在使用base::sample.int函数。因此，目前只有替换抽样是可能的。o在'fracOverlap'函数中增加了一个逻辑参数'both'。 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)