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NEWS
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KAT Changelog
==========================================
V2.4.0 - December 2017
Fully encapsulated boost within KAT, which means boost is no longer an external dependency. Boost is
pulled from github and built during execution of the autogen.sh script. As a side effect this breaks
installation from a tarball, so that option is no longer supported by KAT. Users must clone/pull from
github to build KAT from this release on.
Improved dist analysis script to fix some bugs and support GCP matrix files.
==========================================
V2.3.4 - 11th May 2017
Fixed bug in spectra-cn plotting. Now the user has proper control over selection of cn bands.
==========================================
V2.3.3 - 7th April 2017
Fixed a bug which was causing a seg fault when using the comp tool with bin sizes larger than the default value.
Tweaked header of SECT stats output to make it clearer.
SECT now allows includes lowercase bases in analysis.
Added stack trace if a seg fault occurs
==========================================
V2.3.2 - 7th March 2017
KAT now allows users to pipe in gzipped files via process substitution.
Updated distribution analysis script to make it more robust and added calculations for estimated
genome size and level of heterozygous content.
Fixed a bug in spectra hist plot title.
Fixed a bug in the help message for '-n' option in kat comp.
==========================================
V2.3.1 - 12th December 2016
No changes to the KAT tools themselves. This release focuses on making an improved build process.
User's now have the option of disabling plotting completely, and requesting whether to link to
boost in dynamic mode. We also ensure that KAT only links to python3 rather than python2 if
python2 is the default python installation on the system.
==========================================
V2.3.0 - 6th December 2016
Modified sequence filtering tool so that it can now handle filtering of paired end reads.
==========================================
V2.2.0 - 28th October 2016
Improved README and documentation
Better checking of python dependencies
Enforcing static linking of kat_jellyfish and kat libraries to executable
Better checking of sequence files, now kat can detect fasta and fastq files for kmer counting, even without a known extension.
==========================================
V2.1.1 - 26th July 2016
Updated documentation
Removed dependency on sphinx extensions in order to keep both readthedocs and homebrew happy.
Fixed representation of labels and plotting coordinates based on whether the matrix should be interpretted transposed or not.
Added shebang to python library files, in order for homebrew to be happy including them in the bin directory.
===========================================
V2.1.0 - 21st June 2016
Added filtering tools for filtering k-mer hashes and sequences based on presence
or absence of a set of k-mers.
Enhanced plotting functionality through python matplotlib. Configuration
scripts still allow for gnuplot plotting, if user's don't have matplotlib
available on their system
Added online documentation available at: https://readthedocs.org/projects/kat/
KAT library now available, containing core functionality, such as k-mer
counting (i.e. a simplified interface to jellyfish2).
Fixed automated testing functionality, unit tests operate only on KAT
library code, and system tests operate on KAT tools.
Travis CI integration, checks KAT compiles, passes all tests and can
correctly create a distributable after every commit to github.
Changed jellyfish output artifacts to have a "kat_" prefix which will prevent
incompatibilities with existing jellyfish installations. Also modified all
scripts to include a "kat_" prefix as well.
Converted distanalysis script to be python3 code.
Removed checks permitting .gz extension, jellyfish doesn't directly handle compressed
input.
Updated makefile to put jellyfish headers into a unique directory.
Various bug fixes, performance improvements and tidying up of the codebase.
===========================================
V2.0.8 - 4th December 2015
Modified jellyfish executable to have 'k' suffix to avoid overwriting existing
jellyfish2 installs. Shared libraries and the include directory contains a 'k'
prefix before the version number to avoid the same problem.
Fix some issues with unit tests. Some unit tests removed for jellyfish as these
are not appropriate in the KAT codebase.
Remove any install_hooks and simply treat seqan
8000
as a proper sub project in KAT
with its own Makefile.
===========================================
V2.0.7 - 28th November 2015
Made output type selection an option for all tools that produce plots.
Fixed a bug in the configuration scripts which occurs in some environments
caused by spaces rather than tabs.
===========================================
V2.0.6 - 24th September 2015
More fixes for handling inputs correctly. It seems like in some cases we lost
some globbed paths because the paths went out of scope. I've now forced them to
be shared ptrs which ensures they stick around until the input handler goes out
of scope.
===========================================
V2.0.5 - 22nd September 2015
Fixed a bug with input handling not throwing exceptions properly. The issue
stemmed from globbing the input strings, and not returning any paths if the
files pointed to did not exist. The fix is to ensure globbing returns the
originally specified path if nothing else is returned.
Added additional fields to sect stats output. Now include number and percent of
invalid bases in sequence, plus percent non zero after accounting for invalid
bases.
Fixed a bug in SECT when handling sequences with length less than that of kmer
length.
===========================================
V2.0.4 - 26th August 2015
Added ability in the comp tool to handle multiple input files listed explicitly
and separated by spaces.
Fixed an issue checking for gnuplot during configure.
===========================================
V2.0.3 - 21st August 2015
Removed user option to calculate mean or median in sect, now we just add mean
and median to the output anyway.
Added additional output to the sect stats file. Now outputs # zero count bases
for each sequence and the percentage of bases that have some coverage in the
sequence.
Fix error which sometimes occurs when creating output directories
Fixed a bug which meant we can't handle non canonical bases in sequences passed
to sect.
===========================================
V2.0.2 - 19th August 2015
Removed an unecessary include directive, which made it difficult to compile on
various Mac platforms.
===========================================
V2.0.1 - 12th August 2015
Overhauled code base to incorperate jellyfish 2 and seqan, meaning these bits
of software are no longer external dependencies.
Can now k-mer count directly from the KAT tools, simplifying the workflow
Various bugfixes and optimisations.
===========================================
V1.0.7 - 24th March 2015
New functionality for sect: ability to request median coverage for each sequence
rather than the mean. This tends to give much better results as occasionally we
have a few kmers with extremely high coverage in a sequence which skews the mean
coverage.
Fixed a bug in the configuration. Now correctly includes pthread library when
linking the kat and test binaries.
===========================================
V1.0.6 - 17th October 2014
Fixed a bug with the spectra-cn plots where we duplicated the entry for the
highest copy number displayed before combining all together.
Added a feature to spectra-cn so that we can show cumulative increases in
distinct kmers as kmer coverage increases.
Updated Jellyfish version requirement to 1.1.11
===========================================
V1.0.5 - 28th April 2014
Removed call to auto configure when running the autogen.sh script.
Fixed issue where title could not be overriden by the user in the plotting
tools.
Changed short option name for the "list" option in spectra-mx plot tool to
'c'. This is to avoid a conflict with the "title" option.
Provided a more descriptive error message if the user enters a malformed
value for the "list" option in the spectra-mx tool.
Removed call to set the size ratio to 1 in the spectra-mx tool
===========================================
V1.0.4 (internal release) - 1st April 2014
Dropped autoconf version to 2.59 to allow KAT to run in more environments.
Changed floats to doubles in sect. Previously, we may have got imprecise
mean coverage estimates when using really big sequences, such as whole
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chromosome length.
Fixed spectra-cn issue, where we were not including all high copy kmers in a
final band of the spectra-cn plot.
===========================================
V1.0.3 - 28th November 2013
Fixed an overflow bug with SECT, where sequences of over 64K in length, were
not handled correctly.
Fixed an issue with the gnuplot handler, which prevented compilation on Mac
Added and fixed unit tests. Unit tests can now be run by typing "make check"
assuming the boost unit test framework is installed.
Overhauled build system. Added more dependency checks. Added ability to
access dependencies in non-standard locations. Removed auto-generated files
from repository (configure script can be regenerated with "autogen.sh")
===========================================
V1.0.2 - 8th October 2013
Fix to installation procedure when cloning a fresh repository.
- Modified compiler options so that -all-static is off
- Added Makefile.in to git repo
- Modified README to emphasise that only 1.1.10 works with this version.
Fix to spectra-hist so that x-max can be properly adjusted when logscale is on
===========================================
V1.0.1 - 3rd October 2013
Initial Release of KAT.
===========================================