Finish Release-2.4.2

This release contain multiple improvements to the build system, which should make KAT easier to install via several package managers and in other linux desktop environments.

 - support for use of Makefile variable DESTDIR
 - more consistent management for embedding python scripts and installation of python modules
 - minor tweaks to help messages and documentation.
 - both pdf and html are no longer built and installed by default but can be made on request.

Finish Release-2.4.1

Fixing bug with spectra-mx plotting script

Overhauled dist_analysis script and automatically execute this as par…

…t of hist, gcp and comp. Statistics generated are output to stdout as well as a file called .dist_analysis.json for easy parsing in downstream tasks.

Added a new tool called 'cold' for contig length and duplication analysis. This creates a scatter plot where contigs are defined according to their length, kmer duplication rate (in assembly), kmer coverage (according to reads) and GC values.

KAT now supports gzipped fastq and fasta files natively (for k-mer counting only)

KAT can automatically trim the start of reads to a defined number of bases. This is useful for processing 10X data to avoid the barcodes on R1.

Simplified and improved build system:

a subset of boost is kept in the KAT source tree and can be built prior to KAT with a single command: './build_boost.sh'. This version of boost will be statically linked into the KAT binaries and will NOT be installed to the system.

Tweaked compiler options, and ensure KAT builds with GCC 5-7.

kat python scripts are now wrapped up in a proper python package called kat. This is installed along with the kat c++ programs during install to the defined location.

We try to statically link now to most dependencies where practical.

Tidied up user interfaces. Removed "canonical" options, we assume the user wants canonical kmer counting by default.

Finish Hotfix-4

Fixing a bug that occured when trying to run kat from src dir.

Finish Hotfix-3

Finish Hotfix-2

Ensuring any exceptions coming back form local optimisation are dealt with correctly.

Finish Hotfix-1

Fixed python3 detection.

Finish Release-2.3.4

Fixed bug in spectra-cn plotting.  Now the user has proper control over selection of cn bands.

Finish Release-2.3.3

- 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

Finish Release-2.3.2

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 heterozygos content.

Fixed a bug in spectra hist plot title.

Fixed a bug in the help message for '-n' option in kat comp.