#! /usr/bin/env ruby

def readfasta( fp, name, seq )
        nseq = 0
        tmpseq = ""
        while fp.gets
                if $_ =~ /^>/ then
                        name.push( $_.sub(/>/,"").strip )
                        seq.push( tmpseq ) if nseq > 0
                        nseq += 1
                        tmpseq = ""
                else
                        tmpseq += $_.strip
                end
        end
        seq.push( tmpseq )
        return nseq
end



tname = []
tseq = []
infp = File.open( ARGV[0], "r" )
tin = readfasta( infp, tname, tseq )
infp.close
ref = tseq[0]


puts "# posinaln posinref aainref changes"
puts "# changes < 0 means the site is gap in ref"
len = ref.length

for i in 1..(tin-1) # EXCLUDE FIRST SEQUENCE (human)
	for j in 0..(len-1)
		if tseq[i][j..j] == '-' then
			tseq[i][j..j] = 'X'
		else
			break
		end
	end
	for j in 0..(len-1)
		p = len-1-j
		if tseq[i][p..p] == '-' then
			tseq[i][p..p] = 'X'
		else
			break
		end
	end
end

#for i in 0..(tin-1)
#	puts ">"
#	puts tseq[i]
#end
#
#exit

posinref = 0
for posinaln in 0..(len-1)
	column = []
	for i in 1..(tin-1) # EXCLUDE FIRST SEQUENCE
		column.push( tseq[i][posinaln] ) unless tseq[i][posinaln..posinaln] == 'X'
	end
	column.uniq!
#	p column
	changes = column.length
	changes *= -1 if ref[posinaln..posinaln] == '-'
#	p ref[posinaln..posinaln]
	puts (posinaln+1).to_s + "\t" + (posinref+1).to_s + "\t" + ref[posinaln..posinaln] + "\t" + (changes).to_s + "->" + column.join()
	posinref += 1 if ref[posinaln..posinaln] != '-'
end