A script to convert an intervals file into a sorted unoverlapping intervals file. Super fast implementation using multiple hashes, should do the job instantly no matter how big the intervals are.

ps: this utility is similar to -im on GATK, but for queue scripts we need the intervals file fixed before we can run Unified Genotyper because of scatter-gather.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5117 348d0f76-0448-11de-a6fe-93d51630548a

lua/MergeIntervals.lua

@@ -0,0 +1,61 @@
+-- Merges all intervals into a sorted list of unoverlapping intervals
+-- 
+-- ps: this utility is similar to -im on GATK, but for queue scripts we need the intervals
+--     file fixed before we can run Unified Genotyper because of scatter-gather.
+--
+--	Usage:
+--		lua MergeIntervals.lua raw.intervals > merged.intervals
+--
+
+assert(table.getn(arg) > 0, "\n\nMissing input file\n\nUsage:\n\tlua MergeIntervals.lua raw.intervals > merged.intervals\n\n")
+
+-- read file and create chromosome tables with raw intervals marked as "x"
+local intervals = {}
+local intervalKeys = {}
+for l in io.lines(arg[1]) do
+	local chr, a, b = l:match("([%l%d]+):(%d+)-(%d+)")
+	a,b = tonumber(a), tonumber(b)
+	if not intervals[chr] then 
+		intervals[chr] = {}
+		intervals[chr].min = a
+		intervals[chr].max = b
+		intervalKeys[chr] = {}
+	end
+	for i=a,b do intervals[chr][i] = "x" end
+	intervals[chr].min = math.min(intervals[chr].min, a)
+	intervals[chr].max = math.max(intervals[chr].max, b)
+	table.insert(intervalKeys[chr], a)
+end
+
+local intervalSize = {}
+local intervalsIndex = {}
+for c, chrTable in pairs(intervals) do
+	intervalSize[c] = {}
+	intervalsIndex[c] = {}
+	local intervalStart = -1
+	local lastPositionRead = -1
+	table.sort(intervalKeys[c])
+	for _,startKey in ipairs(intervalKeys[c]) do
+		local i = startKey
+		while chrTable[i] and i > lastPositionRead do
+			if (intervalStart < 0 or i ~= (intervalStart + intervalSize[c][intervalStart] + 1)) then 
+				intervalStart = i
+				intervalSize[c][intervalStart] = 0 
+				table.insert(intervalsIndex[c], intervalStart)
+			else 
+				intervalSize[c][intervalStart] = intervalSize[c][intervalStart] + 1
+			end
+			lastPositionRead = i
+			i = i + 1
+		end
+	end
+end
+
+for c,v in pairs(intervalsIndex) do
+	table.sort(v)
+	for _,intervalStart in ipairs(v) do
+		if intervalSize[c][intervalStart] > 0 then 
+			print(c..":"..intervalStart.."-"..intervalStart + intervalSize[c][intervalStart])
+		end
+	end
+end