v1.48.1

1. Fixed a bug in the launch script which meant that memory
   settings weren't detected correctly unless java was
   installed on the system.

2. Made all preferences for the read count quantitation be
   remembered between runs.

3. Removed spurious additional label in the BAM file import
   options dialog.

4. Don't add projects which fail to load to the recently used
   file list.

5. Update install instructions for M1 mac users.

v1.48.0

A mix of bugfixes and some internal restructuring

1. Fixed the crash reporter which couldn't cope with https URLs

2. Changed the cache folder code to reduce the number of files
   created in a single directory.

3. Added an option to the BAM file import to bring in data
   which has barcodes or sample names embedded in the read IDs

4. Show the strand in the feature search results.

5. Vastly improve the speed of switching chromosomes or resizing
   the chromosome view when lots of tracks are being displayed.

v1.47.2

1. Fix cache crash in seqmonk_import

2. Add java executable detection to seqmonk_import

3. Increase min R version to 4.0.3 because of bioconductor changes

4. Fix OSX launcher to work on older version of OSX

5. Allow 1-to-many comparisons in the DESeq filter

6. Fix stored filter preferences crash

7. Fix edge case mistake in feature filter overlaps

8. Automatically detect new OSX R Framework location

9. Update name cache when renaming features

v1.47.1

This version contains some minor fixes.

Changes include:

1. Increased the minimum R version to 4.x.x. since R3.6 no longer
   works for installing BioConductor packages.

2. Hopefully finally stop OSX from trying to compile R packages
   from source when it doesn't need to.

3. Improve the efficiency of displaying annotation counts

4. Make genomes with annotation versions >99 sort correctly

5. Increase the number of allowed nodes in the probe list overlap
   plot to 500

6. Add more options to the logistic regression filter

v1.47.0

This version introduces some major changes for users of Mac OSX
and improves a lot of existing functionality.

There are two major changes of note:

1. The way the OSX package is built has been changed so that we can
   deal with the new security model in OSX v10.15 (Catalina). People
   working on that version will have found that they were unable to
   load or save data to anywhere other than their home directory.
   This new version now tests for limited disk access on OSX and if
   it finds it it will point to instructions for how SeqMonk can be
   given more generous permissions to read data from places like USB
   drives, network shares and the Desktop.

2. We've made a relatively minor change to the way that RNA-Seq
   quantitation works. When we merge transcript isoforms we used to
   prefer matching transcripts based on them having compatible names
   (eg ABC-201 would merge with ABC-202), and based on them actually
   overlapping in the genome. We found though that some gene models
   from Ensembl broke these assumptions (ie there are cases with
   two different genes with identical names which overlap, and cases
   of genes with multiple transcripts which don't overlap). These
   cases are all nuts but they exist so we need to deal with them. We've
   now changed to prefer using the "gene_id" annotation on transcripts
   to decide which ones to merge, which deals better with these edge
   cases. What this means though is that if you have an existing
   RNA-Seq analysis in a project and you re-quantitate it having moved
   to the new SeqMonk version that your probe set will be replaced as
   it won't match the exsting set because of these changes. You will
   therefore need to either re-create your filtered lists using the
   new probe set - or stick to an older version of SeqMonk to finish
   off those existing projects.

Other more minor changes are:

3. Improve the default matching options and save name for annotated
   probe reports.

4. Added a vistory event for adding annotation

5. Added replicate set colouring to boxplots and beanplots

6. Made the default heatmap colours more friendly to colourblind people

7. Changed the min R version to 3.6 as Bioconductor is broken for
   versions older than that.

8. Fixed a StarWars layout bug for multiple lists and one store.

9. Use https to communicate with web services

10. Try to improve R package installs on OSX

v1.46.0

The v1.46.0 release introduces a couple of new features and fixes
some bugs.

The main changes are:

1. In statistical tests which can use more than 2 replicate sets
   we now remember the order of selection of the sets in the options
   so that the meaning of the fold change values is deterministic, ie
   if you are comparing WT and KO you can choose to have the change as
   either WT/KO or KO/WT in the report.

2. Fixed a bug where the intersect lists filter could make project files
   which couldn't be re-loaded.

3. Added suitable track headers to make exported BED files more compatible
   with UCSC browser

4. Allowed custom distances for "not close to" feature filter

5. Added an option to define co-factors when constructing a linear model
   for DESeq2.

6. Fixed the save data option in the quantitation trend heatmap

7. Fixed PCA domain quantitation probe generation

8. Added the current quantitation values to the HiC report

9. Make the annotation set name the same as the feature name for imported
   annotation.

10. Made the linux launch script SLURM aware so it configures memory limits
    correctly.

11. Fix the warning of replacing probes in the RNA-Seq quantitation pipeline
    so it only warns if it's actually going to replace them.

12. In DESeq2 pairwise comparisons we now report both the raw log2FoldChange
    and the shrunken log2FoldChange.

v1.45.4

RELEASE NOTES FOR SeqMonk v1.45.4

This release is a bugfix release for the last version which resolves
an issue where small probes might not be drawn in the chromsome view
if their inferred size was less than 1 pixel.

It also introduces a copule of other minor changes:

1. Fix a probe drawing optimisation bug which caused some small probes
   not to be drawn.

2. Add the option to highlight replicate sets in the line graph.

3. Annotate the variance filter results with the actual variance
   values which were used for the test.

4. Improved the efficiency of drawing raw reads in the chromosome view
   for replicate sets and data groups.

v1.45.3

RELEASE NOTES FOR SeqMonk v1.45.3

This release adds some useful functionality and cleans up a lot of
the new functions which have been added in recent releases. The main
changes are:

1. Indexed colours now duplicate if you're looking at expanded
   replicate sets

2. Genome view block display now works

3. Added an option to apply the same manual correction to all samples

4. Added an option to make an annotation track instead of a probe set
   for all probe generators

5. Allow probe sets to be called something other than "All Probes"

6. Allow annotated probe reports to be annotated with list values from
   any combination of probe lists

7. Allow any images to be pasted into Vistories

8. Added a --introns option to the command line importer

9. Fixed per-probe normalisation when the "Use visible stores" option is
   selected

10. Added the ability to label multiple points in all scatterplot type
    displays

11. Added a new normalisation method based on subtracting a linear
    trend from your data

12. Added a "sum" and "divide" option to to per-probe normalisation

13. Make seqmonk prompt on exit if a vistory has been modified and
    viewed but not saved.

14. Allow all graphics exports to go straight to the clipboard

15. Created a vistory event for hierarchical cluster probe generation

v1.45.2

RELEASE NOTES FOR SeqMonk v1.45.2

This is a bugfix and stability release which tidies up a number of
areas. The main changes are:

1. Update vistory filter events to have the number of probes and
   the name of the filter attached to them.

2. Fix a versioning bug when cross-importing annotation from another
   project. Also allow cross importing between different annotation
   versions of the same genome assembly.

3. Added a duplicate list filter which makes it easier to create
   additional structure in a set of filtered probes.

4. Allow images to be moved up and down in vistories

5. Make the difference quantitation introduce NA values for ratio
   measures when the total number of observations is very small.

6. Fix an updating bug when changing the number of pseudo chromosomes
   when building a custom genome.

7. When auto-creating Data Groups only add each data set to one group.

8. Allow the creation of projects using just a control genome.

9. Add a save option to the probe list overlap matrix.

10. Improve the description of the percentile value filter.

11. Generate vistory events for probe lists created in plots

12. Add the replicate set name to the plot area in variation plots.

13. Fix the genome view image export to not include scroll bars.

v1.45.1

RELEASE NOTES FOR SeqMonk v1.45.1

This is a bugfix release which resolves some issues in the previous
release. It also adds some minor additional functionality.

Changes in this release are:

1. We fixed a bug in the packaging script for OSX which meant that
   SeqMonk was not using the bundled JRE and was reliant on the
   presence of a Java installation on the host machine. This also
   caused a failure to launch on machines running a version of
   Java older than 1.8.

2. We updated our BAM parser from the old samtools java library to
   the newer htslib parser. This should resolve crashes caused when
   the mapping command line recorded in the BAM header contained a
   colon. Using the newer parser should also be somewhat quicker.

3. We fixed some limitations in Vistories. The table of contents
   in the HTML report won't now truncate on smaller screens. We
   capture some additional events which we were missing before.
   Additional fixes will follow in future releases.

4. We fixed a crash in the List Annotation Value filter.

5. We added a new display option to change how replicate sets treat
   probes which have quantitations for some (but not all) of their
   members. Previously we had returned an NA value for the mean of
   the probe if any member contained an NA. You can now choose to
   return the mean of however many members contain valid values to
   give more complete coverage of your data.