1.5.2版本的变化- - - - - - - - - - - - - - - - - - - - - - - -更新o固定跟踪名称,清除o代码下载SDRFs重命名seq.srdf更新。txt .sdrf。txt o统一功能提供默认选项o暴露过程中使用的选项啊,改变错误警告,过程仍然可以完成o固定不当工具检测外部R云,添加检测使用元素的路径。o简化设置的工具选项,删除后需要调用initEnvironmentVariables选项设置了自动更新的帮助页o由相关的所有选项页面转化为“包选项”页面和“处理选项”页面。暴露所有选项。o把initEnvironmentVariables o删除过时的引用1.5.1版本的变化- - - - - - - - - - - - - - - - - - - - - - - -更新o提高ArrayExpressHTS o stop.on添加错误处理。警告,允许检测可能的失败。然而如果使用它将狭窄的实验能够成功处理。o添加日志。在必要时错误而不是log.info o重组管道的选择,让他们看到用户在命令语法。o重组R云参数到一个组可见/可用选项o了管道自动检测“有机体”SDRF和过滤器使用选定的值。o重做阅读SDRF覆盖大部分的“灵活的格式”情况下o R的改进创造云计算集群,扩大使用重试。 o added proper functions to work with environment variables o updated package help pages o updated the annotation processing following Ensembl update. o updated help pages, descriptions and references o updated package vignette documentation o slightly reorganised the structure of the document o rewritten some sections o added a few new sections o added examples where needed o reimplemented problematic searching and downloading of .seq.sdrf.txt files o fixed problematic handling of "NA" or "missing" nominal length values from ENA o made a number of reference preparation tasks be able to run in parallel and not affect each other. o fixed the "count" method to properly read fields of bam files CHANGES IN VERSION 1.3.1 ------------------------ NEW FEATURES o Added test dataset, which is a cut version of E-GEOD-16190 experiment o Added normalization of the reference folder o Added automatic fixing of reference .fai index, namely duplicated chromosome entries o Added automatic detection of quality scale where possible o Added and option to specify quality scale for custom experiments o Performed performance and memory optimization o Removed options$reference_version. Since the pipeline allows processing of multi-species datasets, a single version cannot fit into multiple organism paradigm. The pipeline always runs on the latest version of reference. Support for custom versions can be added upon request. o Added memory monitoring BUG FIXES o Fixes to accommodate changes in Ensembl interfaces, required for preparation of reference and annotation data. o Fixes to accommodate changes in ENA interfaces, required for querying metadata & downloading datasets for ArrayExpress experiments. o Fixed examples in prepareReference help page o Fixed ArrayExpressHTSFastQ scenario without .sdrf o Fixed production of final alignment report CHANGES IN VERSION 1.3.0 ------------------------ o No changes. Version changed due to package propagation. CHANGES IN VERSION 1.0.1 ------------------------ NEW FEATURES o added prepareAnnotation and prepareReference functions o reworked the discovery of reference data o updated the package after upgrading R and related packages on the EBI R-Cloud BUG FIXES o Fixed computation of insert size for paired end experiments o Fixed fltbam tool that was not part of the pipeline and could not be invoked o Fixed plot_scatter_samples calling to_expressionset with wrong argumenta o Fixed problems with graphics after upgrade of R and graphics subsystem