binBamReads

#!/usr/bin/env ruby

if (ARGV.size != 1)
	STDERR.printf("Usage: %s bam-file\n", File.basename($0))
	exit(1)
end

bam, rest  = ARGV

goodPaired = 0
pairMap1 = Hash.new
pairMap2 = Hash.new
`samtools view #{bam}`.split("\n").each do |line|
	name, flag, contig = line.chomp.split("\t")
	if (name[1] == "1")
		pairMap1[name] = contig
		pairMap2[name] = "*" if (!pairMap2[name])
	else
		name[1] = "1"
		pairMap2[name] = contig
		pairMap1[name] = "*" if (!pairMap1[name])
	end
end

fname = File.basename(bam, ".bam")
mismatch = File.new(fname + ".mismatch", "w")
unpaired = File.new(fname + ".unpaired", "w")
unmapped = File.new(fname + ".unmapped", "w")

pairMap1.keys.sort.each do |key|
	if (pairMap1[key] != pairMap2[key] && pairMap1[key] != "*" && pairMap2[key] != "*")
		key2 = key.dup
		key2[1] = "2"
		mismatch.printf("%s\t%s\t%s\t%s\n", key, key2, pairMap1[key],pairMap2[key])
        elsif(pairMap1[key] == "*" && pairMap2[key] == "*")
          	unmapped.printf("%s\t%s\t%s\t%s\n", key, key2, pairMap1[key],pairMap2[key])
	elsif(pairMap1[key] == "*" || pairMap2[key] == "*")
		unpaired.printf("%s\t%s\t%s\t%s\n", key, key2, pairMap1[key],pairMap2[key])
	end
end
mismatch.close
unpaired.close
unmapped.close


STDERR.printf("There are %d pairs", pairMap1.keys.size)