diff --git a/lua/IntervalUtils.lua b/lua/IntervalUtils.lua
new file mode 100644
index 000000000..dc377d7f7
--- /dev/null
+++ b/lua/IntervalUtils.lua
@@ -0,0 +1,140 @@
+------------------------------------------------------------------------------------------------------------------------
+-- Creates a new interval table
+--
+-- Return values:
+-- 1: Interval table
+------------------------------------------------------------------------------------------------------------------------
+
+function newInterval(chr, start, finish, strand, info)
+  return {chr= chr, start=tonumber(start), finish=tonumber(finish), strand=strand, info=info}
+end
+
+
+------------------------------------------------------------------------------------------------------------------------
+-- Parses a line from an interval list file (not a header line!)
+--
+-- Return values:
+-- 1: chromosome
+-- 2: interval start
+-- 3: interval end
+-- 4: strand (+/-)
+-- 5: info field
+------------------------------------------------------------------------------------------------------------------------
+local function parseIntervalLine(l)
+  return l:match("(%w+)%s+(%d+)%s+(%d+)%s+([%+%-])%s+(.*)")
+end
+
+------------------------------------------------------------------------------------------------------------------------
+-- Reads an interval list file into a table
+--
+-- Return values:
+-- 1: table of intervals
+-- 2: header string
+------------------------------------------------------------------------------------------------------------------------
+local function readIntervalList(filename)
+  t = {}
+  header = ""
+  for l in io.lines(filename) do
+    if l:sub(1,1) == "@" then header = header .. l .."\n"
+    else
+        local chr, start, finish, strand, info = parseIntervalLine(l)
+        table.insert(t, newInterval(chr, start, finish, strand, info))
+    end
+  end
+  return t, header
+end
+
+------------------------------------------------------------------------------------------------------------------------
+-- Checks if two intervals have the same chromosome, start and end.
+--
+-- Return values:
+-- 1: true/false
+------------------------------------------------------------------------------------------------------------------------
+local function isSameInterval (i1, i2)
+  return i1.chr == i2.chr and i1.start == i2.start and i1.finish == i2.finish
+end
+
+------------------------------------------------------------------------------------------------------------------------
+-- Checks if the line from an interval list file is a header line
+--
+-- Return values:
+-- 1: true/false
+------------------------------------------------------------------------------------------------------------------------
+local function isIntervalHeaderLine(l)
+  return l:sub(1,1) == "@"
+end
+
+
+------------------------------------------------------------------------------------------------------------------------
+-- Compares the start position of two intervals
+--
+-- Return values:
+-- 1: -1, 0 or 1 (respectively for a < b, a == b, a > b)
+------------------------------------------------------------------------------------------------------------------------
+local function compIntervals(a, b)
+
+  local function c(x,y)
+    if x < y then return -1
+    elseif x > y then return 1
+    else return 0 end
+  end
+  -- same chromosomes
+  if a.chr == b.chr then return c(a.start, b.start)
+  else
+    x = tonumber(a.chr)
+    y = tonumber(b.chr)
+    if x and y then return c(x,y)
+    else return c(a.chr, b.chr) end
+  end
+end
+
+------------------------------------------------------------------------------------------------------------------------
+-- Compare function to sort a list of intervals (use with table.sort)
+--
+-- Return values:
+-- 1: true if a < b, false otherwise.
+------------------------------------------------------------------------------------------------------------------------
+local function sortCompInterval(a, b)
+  if a.chr == b.chr then return a.start < b.start end
+  local x = tonumber(a.chr)
+  local y = tonumber(b.chr)
+  if x and y then
+    return x < y end
+  return a.chr < b.chr
+end
+
+------------------------------------------------------------------------------------------------------------------------
+-- Checks if the interval is a valid human genome interval
+--
+-- Return values:
+-- 1: true/false
+------------------------------------------------------------------------------------------------------------------------
+local function isValidInterval(interval)
+  local x
+  if interval.chr == "X" then x = 23
+  elseif interval.chr == "Y" then x = 24
+  elseif interval.chr == "MT" then x = 25
+  else x = tonumber(interval.chr) end
+  return x >= 1 and x <= 25 and interval.start < interval.finish and chr_limits[x] > interval.finish
+end
+
+
+------------------------------------------------------------------------------------------------------------------------
+-- Checks if the intervals are overlapping. Intervals are said to overlap if one of the following is true:
+-- i1i2: i1 starts before i2, but ends inside i2.
+-- i2i1: i2 starts before i1, but ends inside i1.
+-- i1_inside: i1 is fully contained inside i2.
+-- i2_inside: i2 is fully contained inside i1.
+--
+-- Return values:
+-- 1: true/false
+-- 2: if true, returns "i1i2", "i2i1", "i1_inside", "i2_inside"
+------------------------------------------------------------------------------------------------------------------------
+local function isOverlappingInterval(i1, i2)
+  if i1.chr ~= i2.chr then return false
+  elseif i1.start < i2.start and i1.finish < i2.finish then return true, "i1i2"
+  elseif i2.start < i1.start and i2.finish < i1.finish then return true, "i2i1"
+  elseif i1.start > i2.start and i1.finish < i2.finish then return true, "i1_inside"
+  elseif i2.start > i1.start and i2.finish < i1.finish then return true, "i2_inside"
+  else return false end
+end
\ No newline at end of file
diff --git a/lua/hasTheseTargets.lua b/lua/hasTheseTargets.lua
index 912bb7cc4..3a6682de1 100644
--- a/lua/hasTheseTargets.lua
+++ b/lua/hasTheseTargets.lua
@@ -114,8 +114,6 @@ local function findInterval(i, intervals)
   local finish = table.getn(intervals)
   local current = math.floor((start + finish) / 2)
 
---  print("findInterval: ", start, finish, current, intervals[current].c, intervals[current].s, intervals[current].e)
-
   while start < finish and not intervalContainsInterval(i, intervals[current]) and not isInterceptingInterval(i, intervals[current]) do
     if compIntervals(i, intervals[current]) < 0 then
       finish = current - 1
@@ -123,7 +121,6 @@ local function findInterval(i, intervals)
       start = current + 1
     end
     current = math.floor((start + finish) / 2)
---    print("findInterval: ", start, finish, current, intervals[current].c, intervals[current].s, intervals[current].e)
   end
   return intervalContainsInterval(i, intervals[current]), current
 end
@@ -138,7 +135,6 @@ for l in io.lines(targetSet) do
   if not isIntervalHeaderLine(l) then
     local c, s, e, st, info = parseIntervalLine(l)
     local intA = newInterval(c,s,e,st,info)
---    print("Debug: ", c,s,e,info)
     local intervalExists, i = findInterval(intA, a)
     if intervalExists then
       print(a[i].c, a[i].s, a[i].e, st, info)
diff --git a/lua/sortGenesByCoverage.lua b/lua/sortGenesByCoverage.lua
index 4bbf2b364..6860976fe 100644
--- a/lua/sortGenesByCoverage.lua
+++ b/lua/sortGenesByCoverage.lua
@@ -8,7 +8,7 @@
 -- Global script variables
 -------------------------------------------------------------------------------
 local coverage = arg[1]
-local genesOfInterest= arg[2] or "/Volumes/humgen/gsa-hpprojects/dev/carneiro/top_genes/data/disease.genes.annotated.interval_list"
+local genesOfInterest= arg[2]
 
 local genes = {}
 local header = ""
@@ -33,7 +33,6 @@ for l in io.lines(genesOfInterest) do
   if l:sub(1,1) == "@" then header = header .. l .."\n"
   else
     local c, s, e, info = l:match("(%w+)%s+(%d+)%s+(%d+)%s+%+%s+(.*)")
---    print("Debug: adding gene: ",c,s,e,info)
     table.insert(genes, {c=c, s=tonumber(s), e=tonumber(e), info=info})
   end
 end
@@ -46,7 +45,6 @@ for l in io.lines(coverage) do
     s = tonumber(s)
     e = tonumber(e)
     while genes[i] ~= nil and (isSameGene(i, c, s, e) or isMergedGene(i, c, s, e)) do
---      print("Debug: ", c, s, e, "--",genes[i].c, genes[i].s, genes[i].e)
       genes[i].totalCoverage = tonumber(totalCoverage)
       genes[i].avgCoverage = tonumber(avgCoverage)
       geneOk = true