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added some comments

This commit is contained in:
Heng Li 2011-04-18 01:47:51 -04:00
parent b09ca93584
commit 8cc5761f65
1 changed files with 10 additions and 10 deletions
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20
lua/bio.lua
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@ -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