1. tss101
  2. optiCall

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<tsh...@gmail.com  committed f4ea7df

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-== Welcome ==
-
-Welcome to your wiki! This is the default page we've installed for your convenience. Go ahead and edit it.
-
-=== Wiki features ===
-
-This wiki uses the [[http://www.wikicreole.org/|Creole]] syntax, and is fully compatible with the 1.0 specification.
-
-The wiki itself is actually a hg repository, which means you can clone it, edit it locally/offline, add images or any other file type, and push it back to us. It will be live immediately.
-
-Go ahead and try:
-
-{{{
-$ hg clone http://bitbucket.org/tss101/opticall/wiki
-}}}
-
-Wiki pages are normal files, with the .wiki extension. You can edit them locally, as well as creating new ones.
-
-=== Syntax highlighting ===
-
-You can also highlight snippets of text, we use the excellent [[http://www.pygments.org/|Pygments]] library.
-
-Here's an example of some Python code:
-
-{{{
-#!python
-
-def wiki_rocks(text):
-	formatter = lambda t: "funky"+t
-	return formatter(text)
-}}}
-
-You can check out the source of this page to see how that's done, and make sure to bookmark [[http://pygments.org/docs/lexers/|the vast library of Pygment lexers]], we accept the 'short name' or the 'mimetype' of anything in there.
-
-Have fun!
+
+
+USAGE
+            opticall [options] [-in INPUT_FILE] [-out OUTPUT_FILE]
+ 
+ 
+DESCRIPTION
+ 
+The code reads in a text file (columns: rs, coord, allelesAB, id_1a, id_1b, id_2a, id_2b, etc), and iterates using an EM algorithm to a convergent set of calls. 
+ 
+
+ 
+ 
+OPTIONS
+ 
+            -in FILE
+ 
+The input file name, in the format 
+ 
+            -out FILE
+ 
+The output file name. This will have the suffix '.calls' appended to it for the genotype calls and '.probs' for the posterior probabilities. The output format is space-delimited with columns: coordinate, rs, perturbation score, allelesAB, call_1, call_2, call_3,.... The order of the calls is the same as the header from the input file. The calls are encoded as 1 = AA, 2 = AB (heterozygote), 3 = BB, 4 = NN (no call).
+