v1.45.0

RELEASE NOTES FOR SeqMonk v1.45.0

SeqMonk v1.45.0 is a major release which introduces some big changes
in the program.

The two major changes with this release are:

1. The introduction of Vistories, which are a way of documenting
   your SeqMonk analysis. This is a document mixing the automatic
   collection of events in the program with embedding graphics and
   tables and allowing you to annotate the analysis with titles
   and text. Vistories can be saved and loaded and can be exported
   to HTML files for archiving and distribution.

2. With the change in licensing of the Oracle JRE we have made the
   decision to stop relying on a JRE on the host computer and are
   instead shipping embedded copies of the AdoptOpenJDK distributions
   of java along with SeqMonk. This means that we now have platform
   specific versions of SeqMonk for Windows, Linux and OSX, and that
   the install procedure is much simpler than before since java is
   no longer required to be separately installed.

In addition to these major features we have added a number of other
changes in this release.

• The LIMMA filter can now analyse multiple replicate sets in a single
  operation.

• A bug in the Probe Trend plot when using the "scale within each
  data store" option was fixed.

• We have removed the option to allow the storage of uncompressed
  project files. In future all project files will be compressed.

• The list annotation filter can now use annotations coming from
  lists other than the one you are filtering.

v1.44.0

This release makes a major change in the way that probe lists annotations
are handled to make them much more flexible. It also introduces some
new filtering, visualisation and reporting options as well as fixing
a bug in the read position probe generator.

Major changes are:

• Probe lists can now record multiple named attributes (and can have
  no attribute at all). This means that a statistical filter can now
  record a p-value, q-value and fold change all together in the same
  list for example.

• Added a probe list annotation value filter to allow for additional
  filtering based on the contents of a probe lists annotations.

• Updated the DESeq and EdgeR, LIMMA, T-test/ANOVA, Intensity Diff
  filters to record p-value,q-value and log2 fold change.

• Added a volcano plot to visualise hits for statistical search
  result lists. Works for DESeq and EdgeR at the moment and will
  support more tests in future.

• Added a custom layout for the chromosome view to more efficiently
  handle the structure of the tracks, especially where there are
  large numbers of tracks in a project.

• Added an option to do bulk renaming of data stores to the DataSet
  editor

• Improved the layout of data tracks when there are a lot of them

• Added a track number to the data track selector

• Fixed a bug in the read position probe generator which meant that
  reads on different strands were counted separately even if the
  ignore strand option was selected

• Added fastseg to the R package requirements to make sure its there
  for people using the segmentation tool

• Made changes to improve the speed of project saving

• Fixed a crash in the PCA plot when the data contains no variance

• Added an option to export annotation tracks as a BED file

• Added a match by name option to the feature report

• Added a generic NOT option to all feature filter matching types

• Updated the R installer code to respect a locally set preferred
  CRAN repository, and to use the new BiocManager to install
  bioconductor packages if appropriate.

v1.43.0

RELEASE NOTES FOR SeqMonk v1.43.0

This release adds some interesting new functionality for segregating
quantitation, and has some speed improvements as well as fixing some
bugs.

Main changes were:

• Fixed a bug which broke data imports in Bed and BedPE format

• Added drawing optimisation to the chromosome view to make it more
  efficient displaying tracks with very high coverage

• Sped up the operation of DataGroups and ReplicateSets when collating
  raw reads

• Added a new intersect lists filter to provide more filtering options
  when combining lists together

• Changed the order of operations when saving files to reduce the
  chances of data loss if something odd happens to the filesystem
  whilst saving

• Improved the efficiency of the read position probe generator

• Added a segmentation filter to split quantitations into physically
  connected groups

• Added the ability to cross import annotation tracks between projects

• Added an annotation editor to make it easy to rename or delete large
  batches of annotation quickly

• Reduced the compression when saving to make it quicker

• Fixed a crash in the variance intensity difference filter if null
  quantitations were present

v1.42.1

RELEASE NOTES FOR SeqMonk v1.42.1

This release was an opportunity for a general cleanup of a lot of cosmetic
issues which had been building up, as well as addressing a number of bugs.

Things which we fixed were:

• Fixed the text alignment on a lot of plot axes to be more pretty

• Fixed a data scaling bug on the QQ plot which sometimes missed out the
  last point

• Fixed a crash in LIMMA when data contained NA values

• Fixed a cancellation bug in the HiC heatmap

• Fixed a null pointer bug in the proportion of library bug

• Added an option to save the data from the quantitation trend plot

• Added whitespace support to generic text import

• We now record the import options used when importing data

• Handle platforms where we can't automatically open a web browser better

• Fixed a bug where the read position probe generator only did a single chromosome

• Improved the layout of the quantitation trend heatmap

• Fixed a bug with NA or infinite values in the quantitation trend plot

v1.42.0

RELEASE NOTES FOR SeqMonk v1.42.0

This release has a fix for a potentially nasty data import bug introduced in
v1.40.1 and adds some new visualisation features.

Important Data Import Bug
#####################

We are indebted to John Chuang for spotting a data import bug which was
introduced in v1.40.1 and which could corrupt data imported from sorted
BAM files containing duplicated sequences. We'll do a full write up
elsewhere but the details of the bug can be seen in:

#99

In short, if you have imported a sorted BAM file using SeqMonk v1.40.1 or
v1.41.0 then you may have had some duplicate reads silently discarded. The
issue could also theoretically affect sorted files, but the number of
sequences affected would be extremely low and is unlikely to materially
affect any datasets.

Projects which had data imported in an earlier version of seqmonk, and the
project was opened and saved in the affected versions are not affected.
The bug is in the import step.

If you imported sorted files into an affected version of the program then
we recommend that you create a new project and re-import the BAM files
using seqmonk v1.42.0 (or later).

Other changes in this release:

• Added a size factor normalisation quantitation

• Fixed a data update bug when creating custom genomes

• Added a new Quantitation Trend Heatmap plot, and optimised the old
  Quantitation Trend Plot code

• Worked around an EdgeR installation bug which caused the EdgeR
  filter to break.

• Fixed a problem with the linux themeing on Ubuntu 18.04

v1.41.0

This release adds some new functionality, but also tidies up a lot of existing
features, making them work more smoothly.

• Added a QQ plot

• Improved the options and multiple testing correction in the logistic
  regression filter.

• Fixed a slowness issue when working with hundreds of samples.

• Added a mechanism to allow projects to update to newer versions of
  core annotations in the same assembly.

• Added a fix for the RNA-Seq QC plot when there isn't a rRNA track in
  the annotation.

• Modified the DESeq filter to allow multiple group comparisons by using
  the Likelihood ratio test.

• Report the parameters estimated by the RNA-Seq pipeline.

v1.40.1

This is a bugfix release of seqmonk which adds some optimisations to the
background data model and fixes a number of bugs.

• Changed the internal data model to store positions and counts separately
  to make the storage of heavily duplicated data much more efficient

• Added a LIMMA statistical filter

• Modified the GTF parser to better deal with the structure of Ensembl
  GTF files.

• Changed all of the launchers so you can pass a file name to open. Allows
  file extensions to be associated with seqmonk so you can open projects
  by double clicking on them.

• Improve the merging of transcripts in the RNA-Seq pipeline to use
  gene ids where they are present in the annotation so we don't get
  spurious merging of overlapping transcripts on the same strand which
  are annotated as belonging to different genes.

• Updated the genome processing scripts so that gene_ids are added to
  all transcripts

• Fixed a crash in the aligned probes plot when no data stores are visible

• Fixed a display bug for the list of features in the feature filter and
  quantitation trend plot.

• Fixed an inefficient packing algorithm when the number of reads was too
  great to be displayed within the available height of the chromosome view.

v1.40.0

RELEASE NOTES FOR SeqMonk v1.40.0

This release does some major reorganisation of the filtering menu as well as
adding new functionality. Major changes are:

• Completely restructured the statistics filter menus so that they are
  now arranged by the type of data they apply to.

• Added an option to detect and remove duplication in the RNA-Seq
  quantitation pipeline.

• Added a new variant of the EdgeR filter which can work on for/rev
  ratio data such as methylation data.

• Added an option to change the startup memory settings from the usual
  preferences dialog.

• Added an R debug mode to make it easier to track down problems with R
  based functionality.

• Fixed a bug in the variation plot for data containing NaN values

• Fixed a regression which meant some functionality didn't work on systems
  running java 1.6

• Added an option to create data groups or replicate sets from pre-prepared
  lists of data store names.

• Added a global correction to the aligned probes plot to make the plots
  more directly comparable.

• Fixed a bug in the exporting of images from the aligned probes plot.

• Collated error messages to help interpreting large numbers of errors.

• Added a strand bias plot

v1.39.0

This release is a mix of new features and bug and usability fixes for existing
features. Major changes are:

• Added the ability to have multiple annotation versions for the same genome
  assembly release. We needed a way to update the annotations used for some of
  the major eukaryotic genomes, when the sequence level assembly hadn't actually
  changed. All genomes can now have multiple versions distinguished by the Ensembl
  release number from which they came. The genome selection interface now shows
  the different annotation versions for the same genome assembly grouped together.

• Added a parser for the BEDPE file format

• Added a better filtering for absolute change to the binomial, chi-square and
  logistic regression filters.

• The hierarchical cluster plot now allows for the highlighting of replicate sets
  at the top.

• The gene set filter now provides the option to use the Kolmogorov-Smirnov test
  as well as the t-test when finding changing gene sets

• Altered the feature filter to allow it to simultaneously use multiple feature tracks

• Improved the scaling of the aligned probes plot so that the absolute numbers reported
  are more meaningful

• Added a scale bar to the aligned probes plot

• Fixed a crash in the PCA plot when no data remained after removing null values

• Fixed a crash when saving results from the correlation matrix

• Fixed a bug which allowed replicate sets to be added to other replicate sets
  when auto-creating sets in the data store tree

v1.38.2

This is a bugfix release which mainly addresses a bug in the most recent
jave release on OSX. Specific changes in this release are:

• Fixed a hang bug specifically triggered in java v1.8_131 when creating
  any report. The bug doesn't affect other platforms, or previous versions
  of the JRE.

• Fixed a problem with the auto-setup of the perplexity setting in the Tsne
  plot which affected projects with fewer than 7 samnples.

• Fixed a bug which caused the intensity gene set plot to not clean up
  temporary probe lists when the list of hits was sorted.