版本1.5.2的更改---------------------------------------------更新o修复跟踪名称，清理o更新了将SDRFS下载到重命名seq.srdf.txt的代码到.sdrf.txt o统一功能提供默认选项o o在该过程中使用的选项o将错误更改为仍可以完成的警告o o固定不正确的工具在外部R云上检测，并使用路径中的元素添加了检测。o简化的工具选项设置，删除了在设置选项后调用启动VarionmentVariables的需求，使其自动o更新的帮助页面o将所有与选项相关的页面组合到“软件包选项”页面和“处理选项”页面中。暴露了所有选项。o removed the initEnvironmentVariables o removed outdated references CHANGES IN VERSION 1.5.1 ------------------------ UPDATES o improved error handling within the ArrayExpressHTS o added stop.warnings允许更早发现可能的故障。但是，如果使用它将缩小可以成功处理的实验量。o在必要时添加log.error而不是log.info o重组管道选项，使命令语法中的用户可见。o将R云参数重新组织为一组可见/可用选项o使管道从SDRF自动检测“有机体”，并使用选定的值过滤器。o从SDRF进行了重新设计的阅读，以涵盖大多数“灵活格式”案例o改进了R云计算集群的创建，扩大了重试的使用。o添加了适当的功能以与环境变量一起使用o更新的软件包帮助页面o更新了Ensembl更新后的注释处理。 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