CHANGES IN VERSION 1.5.2 ------------------------ UPDATES o fixed trace names, cleanup o updated the code downloading SDRFs to rename seq.srdf.txt to .sdrf.txt o unified the functions providing default options o exposed the options that are used in the process o changed errors to warnings where process can still be completed o fixed improper tools detection on the external R Cloud, added detection using elements in PATH. o simplified setting of tools options, removed the need to invoke initEnvironmentVariables after the options are set, made it automatic o updated help pages o composed all options related pages into "package options" page and "processing options" page. Exposed all options. o removed the initEnvironmentVariables o removed outdated references CHANGES IN VERSION 1.5.1 ------------------------ UPDATES o improved error handling within the ArrayExpressHTS o added stop.on.warnings that allows detection of possible failures earlier. However if used it would narrow the amount of experiments that can be successfully processed. o added log.error instead of log.info where necessary o reorganised pipeline options, made them visible to users in the command syntax. o reorganised R Cloud parameters into a single set of visible/usable options o made the pipeline automatically detect "Organism" from SDRF and filter using a selected value. o reworked reading from SDRF to cover most of the "flexible formatting" cases o improved creation of R Cloud computation cluster, widened usage of retries. 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