bamtools filter script for paried end sequences

flag_filter.json

{
	"filters":[
		{ "id":"firstPairForward",
			"alignmentFlag" : "99" },
		{"id":"firstPairReverse",
			"alignmentFlag" : "83"},
		{"id":"secondPairForward",
			"alignmentFlag" : "163"},
		{"id":"secondPairReverse",
			"alignmentFlag" : "147"}
	],
	"rule": "firstPairForward | firstPairReverse | secondPairReverse | secondPairForward"
}