Merge pull request #62 from andrewjpage/master

swap bases in snp tab file and cleanup filenames
Merge pull request #63 from andrewjpage/master

sliding window at half minimum window size
Merge pull request #64 from andrewjpage/master

Updates to coords other minor bugs
Merge pull request #65 from andrewjpage/master

move window in to first snp
Merge pull request #66 from andrewjpage/master

dont move window past size of genome
Merge pull request #67 from andrewjpage/master

new window shifting method and bug with detecting snps
Merge pull request #68 from andrewjpage/master

	 move inwards one at a time, remove gap extending, Bonferroni correction, sliding window 1
propagate unambiguous bases up the tree
Merge pull request #69 from andrewjpage/propagate_unambiguous_bases_up_tree

propagate unambiguous bases up the tree