Updates to coords other minor bugs

Fix coordinates which were off by 1.
Colour blocks only appearing on a leaf node in blue.
Sliding window moves by window_size/2 each time so there are overlapping windows. Justify by reference to Nyquist.
Lower case 'n' considered when propagating gaps after fastml.
Remove double dots in filenames.
Swap parent and child bases in the branch SNPs tab file.
Updated Heng Li's FASTA parsing library.
Bounded an array properly which reduces memory usage.