Updated samtools to 0.1.19

[rsem.git] / sam / misc / r2plot.lua

diff --git a/sam/misc/r2plot.lua b/sam/misc/r2plot.lua
new file mode 100755 (executable)
index 0000000..0a1b9f1
--- /dev/null
+++ b/sam/misc/r2plot.lua
@@ -0,0 +1,83 @@
+#!/usr/bin/env luajit
+
+function string:split(sep, n)
+       local a, start = {}, 1;
+       sep = sep or "%s+";
+       repeat
+               local b, e = self:find(sep, start);
+               if b == nil then
+                       table.insert(a, self:sub(start));
+                       break
+               end
+               a[#a+1] = self:sub(start, b - 1);
+               start = e + 1;
+               if n and #a == n then
+                       table.insert(a, self:sub(start));
+                       break
+               end
+       until start > #self;
+       return a;
+end
+
+function io.xopen(fn, mode)
+       mode = mode or 'r';
+       if fn == nil then return io.stdin;
+       elseif fn == '-' then return (mode == 'r' and io.stdin) or io.stdout;
+       elseif fn:sub(-3) == '.gz' then return (mode == 'r' and io.popen('gzip -dc ' .. fn, 'r')) or io.popen('gzip > ' .. fn, 'w');
+       elseif fn:sub(-4) == '.bz2' then return (mode == 'r' and io.popen('bzip2 -dc ' .. fn, 'r')) or io.popen('bgzip2 > ' .. fn, 'w');
+       else return io.open(fn, mode) end
+end
+
+local eps = {};
+
+function eps.func(fp)
+       fp = fp or io.stdout
+       fp:write("/C { dup 255 and 255 div exch dup -8 bitshift 255 and 255 div 3 1 roll -16 bitshift 255 and 255 div 3 1 roll setrgbcolor } bind def\n")
+       fp:write("/L { 4 2 roll moveto lineto } bind def\n")
+       fp:write("/LX { dup 4 -1 roll exch moveto lineto } bind def\n")
+       fp:write("/LY { dup 4 -1 roll moveto exch lineto } bind def\n")
+       fp:write("/LS { 3 1 roll moveto show } bind def\n")
+       fp:write("/RS { dup stringwidth pop 4 -1 roll exch sub 3 -1 roll moveto show } bind def\n")
+       fp:write("/B { 4 copy 3 1 roll exch 6 2 roll 8 -2 roll moveto lineto lineto lineto closepath } bind def\n")
+end
+
+function eps.font(ft, size, fp)
+       fp = fp or io.stdout
+       fp:write(string.format('/FS %d def\n', size));
+       fp:write('/FS4 FS 4 div def\n');
+       fp:write('/' .. ft .. ' findfont FS scalefont setfont\n');
+end
+
+local scale = 8;
+
+if #arg == 0 then
+       print("Usage: r2plot.lua <in.txt>");
+       os.exit(1)
+end
+
+local fp = io.xopen(arg[1]);
+local n = tonumber(fp:read());
+
+print('%!PS-Adobe-3.0 EPSF-3.0');
+print('%%' .. string.format('BoundingBox: -%d -%d %.3f %.3f\n', 10*scale, scale, (n+1)*scale, (n+1)*scale));
+print(string.format('%.3f setlinewidth', scale));
+print(string.format('/plot { setgray moveto 0 %d rlineto } def', scale));
+print(string.format('/plothalf { setgray moveto 0 %.2f rlineto } def', scale/2));
+eps.func();
+eps.font('Helvetica', scale-1);
+
+local i = 1;
+for l in fp:lines() do
+       local t = l:split('\t');
+       print(string.format("%d %d FS4 add (%s) RS", (i-1)*scale-2, (i-1)*scale, t[1]));
+       for j = 2, #t do
+               if tonumber(t[j]) > 0.01 then
+                       print(string.format('%.2f %.2f %.2f plot stroke', (i-1+.5)*scale, (j-2)*scale, 1.-t[j]));
+               end
+       end
+       i = i + 1;
+end
+for j = 1, 21 do
+       print(string.format('%.2f %.2f %.2f plothalf stroke', -8*scale, (j-1) * scale/2, 1.-(j-1)/20));
+end
+print('showpage');