History¶
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 intosentinel
, containing generic functionalities andsentinel-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 previousApiMessage
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 toprocessRunUpload
and is now expected to returnFuture[ApiPayload \/ RunRecord]
instead ofTry[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 withFuture
, which has resulted in changes across database-related functions to useFuture
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 classesgetStats
andgetAggregateStats
. 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 asnull
when this value is set totrue
. When set tofalse
, 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.