Version 0.2

Release 0.2.0

release date: TBD

Release 0.2.0-beta1

release date: January 25 2016

First beta release of the 0.2 version.

The majority of the change in this version compared to the previous version is internal. Some of the more important changes are:

  • The sentinel package has now been split into sentinel, containing generic functionalities and sentinel-lumc containing LUMC-specific pipeline support. This separation is not yet complete, since a part of the user configuration still refers to LUMC-specific functionalities. Instead, it is meant to pave way for a complete separation which is expected to happen in future versions.
  • A new type for expected errors called ApiPayload was created to replace the previous ApiMessage case class which contains only error messages. In addition to error messages, ApiPayload may also contain a function that returns a specific HTTP error code. This allows for a given error message to always be tied to a specific HTTP error code.
  • The main pipeline upload processing function in RunsProcessorr has been renamed to processRunUpload and is now expected to return Future[ApiPayload \/ RunRecord] instead of Try[BaseRunRecord]. Related to this change, this version also makes heavier use of the scalaz library, most notably its disjunction type. This allows for a nicer composition with Future, which has resulted in changes across database-related functions to use Future as well.
  • The base functions in the StatsProcessor abstract class underwent a major refactor. In this version, the same functionality was achieved using only two generic classes getStats and getAggregateStats. Future versions are expected to bring additional changes most notably to the MapReduce step, since newer versions of MongoDB supports most (if not all) of the metrics using its aggregation framework only.

There are also some indirect changes related to the code:

  • Sentinel now comes with minimum deployment setup using Ansible. This can be optionally run in a Vagrant VM with the provided Vagrantfile.
  • The required MongoDB version is now 3.2 instead of 3.0.

The complete list of changes are available in the commit logs.

The user-visible changes are quite minimum. Aside from some LUMC pipeline-specific changes, the most visible changes are:

  • The library nomenclature has been replaced with read group. The previous use of library was incorrect and the current one is more in-line with popular next-generation sequencing tools.
  • There is now a URL-parameter called displayNull which allows for clients to view missing JSON attributes as null when this value is set to true. When set to false, which is the default value, missing attributes will be omitted completely from the returned JSON payload.

Version 0.1

Release 0.1.3

release date: October 13 2015

Bug fix (upstream) release:

  • Update CollectInsertSizeMetrics summary object. In some cases, it is possible to have a single end alignment still output a CollectInsertSizeMetrics object in the summary file wit null values, as opposed to not having the object at all.

Release 0.1.2

release date: July 14 2015

Bug fix (upstream) release:

  • Improve summary file parsing for Picard CollectAlignmentSummaryMetrics numbers. In some cases, the number of total reads and aligned reads may be 0. In that case, we use the BiopetFlagstat value instead.

Release 0.1.1

release date: July 11 2015

Bug fix release:

  • Fix bug caused by the Gentrap summary format having a different executable entries for JAR and non-JAR files.
  • Documentation improvements (typos, etc.).

Release 0.1.0

release date: July 6 2015

New version:

  • First release of Sentinel, with support of the Gentrap pipeline.