update doco

README.rdoc

@@ -1,20 +1,29 @@
 = bio-gag
 
-Full description goes here
+bio-gag is a biogem for detecting and correcting a particular type of error that occurs/occurred in a particular version of the IonTorrent sequencing kit. Newer versions of these kits do not appear to be affected by this error.
 
-Note: this software is under active development!
+To search for these errors, a pileup of aligned sequences is required. These can be generated either from an assembly or by aligning to a reference, although it has only been tested on de-novo assemblies assembled with newbler. Note that it is probably not optimised due to time constraints combined with the fact they appear to have been fixed in newer kits.
 
 == Installation
 
         gem install bio-gag
 
 == Usage
 
+To use the script, the important options are these:
+
+        gag [options] <pileup_output>
+
+                --lookahead                  Work out if gag predictions are supported by orf predictions being extended [default is just to print out found gag errors]
+                --fix CONSENSUS_FASTA_FILE   Find gag errors in the pileup file, correct them in CONSENSUS_FASTA_FILE, and print to STDOUT the fixed up consensus
+            -g, --gags GAG_FILE              Specify a list of GAG errors to be fixed in tab-separated form (use with --fix, the tab-separated output is from regular output or --lookahead)
+
+
 == Developers
 
 To use the library 
 
-        require 'bio-gag
+        require 'bio-gag'
 
 The API doc is online. For more code examples see also the test files in
 the source tree.

bin/gag

@@ -21,7 +21,22 @@ options = {
   :trace => 'info',
 }
 o = OptionParser.new do |opts|
-  opts.banner = "gag [options] <pileup_output>"
+  opts.banner = "\ngag [options] <pileup_output>\n\n"
+
+
+  opts.on('--lookahead', 'Work out if gag predictions are supported by orf predictions being extended [default is just to print out found gag errors]. There\'s modifed usage too - probably best for you to look at the code if you are using this operation') do |v|
+    options[:operation] = LOOKAHEAD
+  end
+
+  opts.on('--fix CONSENSUS_FASTA_FILE', 'Find gag errors in the pileup file, correct them in CONSENSUS_FASTA_FILE, and print to STDOUT the fixed up consensus') do |v|
+    options[:operation] = FIX
+    options[:fix_file] = v
+  end
+
+  opts.on('-g','--gags GAG_FILE', 'Specify a list of GAG errors to be fixed in tab-separated form (use with --fix, the tab-separated output is from regular output or --lookahead)') do |v|
+    options[:gags_file] = v
+  end
+
 
   opts.on("--logger filename",String,"Log to file (default STDERR)") do | name |
     options[:logger] = name
@@ -38,19 +53,6 @@ o = OptionParser.new do |opts|
   opts.on("-v", "--verbose", "Run verbosely") do |v|
     options[:trace] = 'info'
   end
-
-  opts.on('--lookahead', 'Work out if gag predictions are supported by orf predictions being extended') do |v|
-    options[:operation] = LOOKAHEAD
-  end
-
-  opts.on('--fix CONSENSUS_FASTA_FILE', 'Find gag errors in the pileup file, correct them in CONSENSUS_FASTA_FILE, and print to STDOUT the fixed up consensus') do |v|
-    options[:operation] = FIX
-    options[:fix_file] = v
-  end
-
-  opts.on('-g','--gags GAG_FILE', 'Specify a list of GAG errors to be fixed in tab-separated form (use with --fix, the tab-separated output is from regular output or --lookahead)') do |v|
-    options[:gags_file] = v
-  end
 end.parse!
 
 # Realize settings

lib/bio/db/gag.rb

@@ -2,7 +2,7 @@
 
 class Bio::DB::PileupIterator
   # Find places in this pileup that correspond to GAG errors
-  # * Currently XYX in the consensus (i.e. the first and third bases are the same, and different to the middle one)
+  # * Currently XYX in the consensus (i.e. the first and third bases are the same, and different to the middle one). This is actually probably not optimal.
   # * There is at least 3 reads that have an insertion of base Y next to Y, and are all in the one direction. Can change this with options[:min_disagreeing_absolute]
   # * The 3 or more reads form at least a proportion of 0.1 (i.e. 10%) of all the reads at that position.  Can change this with options[:min_disagreeing_proportion]
   #