Constant sites refactor

Constant sites refactor.

Add output of only count of constant sites

Add output of only count of constant sites for IQTREE. Provided by Peter van Heusden

Default output to STDOUT

v2.4.0

default output to STDOUT

Output Internal reference and pure mode

2.3.1

version

Build portability improvements

This release introduces a slight overhaul of the build system to hopefully make it more compatible with different platforms.

Small changes, some debian related

Various small changes including to assist with debian packaging, addding a "give me the version please" command line argument and accepting a wider range of characters for unknown bases.

Remove trailing tab from VCF

This release removes a trailing tab from the header row of a VCF. Some tools didn't like the tab.

Change VCF output format

Introduces a breaking change to the VCF output format to make it compatible with other tools such as PLINK and PyVCF.

The new format outputs a VCF in GT FORMAT rather than noting Alt Base INFO. An example of this change can be found here: 09dee85