added some comments

diff --git a/lua/bio.lua b/lua/bio.lua
index de6d558c546d8556c77e9c545a3d470bd863c194..8a4f5406054fafd2aaf2b03df5789dc8801a9502 100644 (file)
--- a/lua/bio.lua
+++ b/lua/bio.lua
@@ -85,8 +85,7 @@ end
 local function intvovlp(intv, bits)
        -- sort and merge intervals
        local function intvmerge(intv)
-               local function cmp(a, b) return a[1] < b[1] end
-               table.sort(intv, cmp)
+               table.sort(intv, function(a,b) return a[1] < b[1] end) -- sort by the start
                local b, e, k = -1, -1, 1
                for i = 1, #intv do
                        if e < intv[i][1] then
@@ -97,8 +96,9 @@ local function intvovlp(intv, bits)
                if e >= 0 then intv[k] = {b, e} end
                while #a > k do table.remove(a) end
        end
-
-       bits = bits or 13
+       -- build the index for the list of intervals
+       bits = bits or 13 -- the default bin size is 8192 = 1<<13
+       intvmerge(intv)
        local idx, size, max = {}, math.pow(2, bits), 0
        for i = 1, #a do
                local b = math.modf(intv[i][1] / size)
@@ -110,17 +110,17 @@ local function intvovlp(intv, bits)
 
        return function(_beg, _end)
                local x = math.modf(_beg / size)
-               x = (max < x and max) or x
-               local off = idx[x];
-               if off == nil then
-                       for i = x - 1, 0, -1 do
+               if x > max then return false end
+               local off = idx[x]; -- the start bin
+               if off == nil then -- the following is not the best in efficiency
+                       for i = x - 1, 0, -1 do -- find the minimum bin with a value
                                if idx[i] ~= nil then off = idx[i]; break; end
                        end
                        if off == nil then return false end
                end
-               for i = off, #intv do
+               for i = off, #intv do -- start from off and search for overlaps
                        if intv[i][1] >= _end then return false end
-                       if intv[i][2] > _beg and intv[i][1] < _end then return true end
+                       if intv[i][2] > _beg and intv[i][1] < _end then return true end 
                end
        end
 end