v1.38.1

This is a bugfix release which addresses some issues found in the previous
release. Specifically

• We fixed a performance bug when creating custom genomes from fasta or gff
  files with very large numbers of sequences in them. This would have affected
  people building custom genomes from very fragmented sets of contigs.

• We added a scale bar to the HiC heatmap

• We changed the TSNE code to use Rtnse instead of tsne to work round a bug and
  to improve performance

• We added some more debugging output to the launch script to make it easier to
  debug launching problems

• We fixed a bug in the SplicingEfficiency pipeline affecting genomes with
  non-Ensembl naming schemes

• We fixed a bug in PCA plotting when showing labels in plots with overlapping
  points

v1.38.0

This release adds some new plotting options for data store similarity and greatly improves the workflow for the analysis of splicing as well as adding some more general bug fixes and improvements.

Major changes are:

• Added a TSNE plot for clustering data stores

• Added colouring to the correlation matrix

• Added a logistic regression splicing statistical filter

• Greatly improved the efficiency of the exactly overlap quantitation

• Added strand information to probe reports

• Fixed a bug in the launcher for UTF8 locales

• Fixed a bug in the normalisation of paired end RNA-Seq data

• Fixed a crash in bioconductor installation

v1.37.1

RELEASE NOTES FOR SeqMonk v1.37.1

This release is a minor bugfix release. Updating to this release is only
necessary for people directly affected by one of the bugs below:

• Fixed a bug in the reporting of R errors where the full R trace wasn't
  attached to the crash report making it difficult to identify the cause
  of R problems.
• Fixed a bug in the generation of custom genomes where feature names
  containing a forward slash in their names would cause a failure of the
  feature caching system.
• Fixed an out of date warning in the RNA-Seq pipeline which hadn't been
  updated to the new option names in the BAM import dialog.

v1.37.0

This release adds a lot of new and modified functionality to make the program
easier to use for some common tasks.

The changes in this release are:

• Added an option to the ChiSquare and Logistic Regression statistics to
  resample the read ratios based on a current normalised percentage quantitation.
  Provides lots of new possibilities for the analysis of BS-Seq data.
• Changed the heatmap view to use the currently set positive/negative scale
  when performing euclidean clustering
• Fixed a bug in PCA plotting where NA or infinite quantitated values were
  present
• Rewrote the features filter to make it much more powerful
• Fixed a bug in seqmonk_import if you specified a filename in the current
  directory
• Updated seqmonk_import to allow the import of bismark coverage files
• Fixed error reporting in seqmonk_import
• Hugely optimised the exact overlap quantitation
• Made the status bar show the stand of any highlighted probe
• Allow the crash email to be changed from the preferences dialog
• Added more options to deduplication to account for different duplication types
• Stopped the RNA-Seq QC plot from duplicating prefixes when doing multiple filters

v1.36.0

This release adds one new major piece of functionality to seqmonk and fixes a bug in the bean plot.

The new functionality is a non-interactive import script 'seqmonk_import'. This script allows you to create a new seqmonk project in a completely automated way so that you don't need to launch an interactive session to do your initial data import. This can be really useful where data might be stored on a cluster where interactive sessions are impractical, and will save the hassle of having to transfer all of the BAM files to a local machine to set up the project.

The bug fix affects the high end of the quantitation distribution in beanplots. In some cases probes with counts in the highest bins were being counted multiple times causing the top end of the plot to stretch in a way which didn't actually reflect the distribution of the data. This issue is now fixed.

v1.35.0

RELEASE NOTES FOR SeqMonk v1.35.0

We're having our windows 10 moment. We've finally got fed up of people asking
why we're not at version 1 yet, so you'll see that the version bump is a little
larger than normal on this release. SeqMonk has been plenty stable for several
years already so I guess it's justified.

This release brings in some new features and some updates to existing features
which should make it easier to work with.

• Added a new setup screen the first time the program is run to try to make
  it easier to set sensible locations for the cache and genomes folders.
• Added the ability to generate PCA plots to compare data stores, and use
  the rotations in a given PC to select sets of probes which characterise that
  PC.
• Added a probe list collation filter to make it easy to intersect large
  numbers of probe lists. Renamed the old combine filter to 'logically combine'
• Improved BedGraph export so you can now output multiple files in one go and
  made them immediately compatible with bedGraphToBigWig so you can more easily
  load them into UCSC browser.
• Fixed a bug in the quantitation of probes using the new multi-genome projects
• Added a duplication quantitation
• Cleaned up and removed a load of functions in the menus which we're pretty
  sure no one ever used.
• Fixed a bug on windows systems when the Documents folder was set to be the
  seqmonk genomes folder. Got to learn a lot about the madness of windows
  junction files.
• Allow the per-probe normalisation to use either the median or the mean
• Fixed a bug when importing HiC data from BAM files and applying a MAPQ
  filter.