# HG changeset patch
# User blankenberg
# Date 1422561721 18000
# Node ID d5f866df45ae65c9340fd4cdc099aa939f2e00af
# Parent  3c3ef33b9d5651e2723ec40d857ed85afce42914
Uploaded

diff -r 3c3ef33b9d56 -r d5f866df45ae tools/naive_variant_caller.py
--- a/tools/naive_variant_caller.py	Wed Feb 26 12:37:00 2014 -0500
+++ b/tools/naive_variant_caller.py	Thu Jan 29 15:02:01 2015 -0500
@@ -18,7 +18,7 @@
     parser.add_option( '-d', '--min_support_depth', dest='min_support_depth', action='store', type="int", default=0, help='Minimum number of reads needed to consider a REF/ALT. Default=0.' )
     parser.add_option( '-q', '--min_base_quality', dest='min_base_quality', action='store', type="int", default=None, help='Minimum base quality.' )
     parser.add_option( '-m', '--min_mapping_quality', dest='min_mapping_quality', action='store', type="int", default=None, help='Minimum mapping.' )
-    parser.add_option( '-t', '--coverage_dtype', dest='coverage_dtype', action='store', type="string", default='uint64', help='dtype to use for coverage array' )
+    parser.add_option( '-t', '--coverage_dtype', dest='coverage_dtype', action='store', type="string", default=None, help='dtype to use for coverage array' )
     parser.add_option( '--allow_out_of_bounds_positions', dest='allow_out_of_bounds_positions', action='store_true', default = False, help='Allows out of bounds positions to not throw fatal errors' )
     parser.add_option( '--safe', dest='safe', action='store_true', default = False, help='Perform checks to prevent certain errors. Is slower.' )
     parser.add_option( '--region', dest='region', action='append', type="string", default=[], help='region' )
diff -r 3c3ef33b9d56 -r d5f866df45ae tools/naive_variant_caller.xml
--- a/tools/naive_variant_caller.xml	Wed Feb 26 12:37:00 2014 -0500
+++ b/tools/naive_variant_caller.xml	Thu Jan 29 15:02:01 2015 -0500
@@ -46,10 +46,10 @@
      --allow_out_of_bounds_positions
      
      #if str( $advanced_options.advanced_options_selector ) == "advanced":
-         --coverage_dtype "${advanced_options.coverage_dtype}"
+         #if str( $advanced_options.coverage_dtype ) != "guess":
+             --coverage_dtype "${advanced_options.coverage_dtype}"
+         #end if
          ${advanced_options.safe}
-     #else
-         --coverage_dtype "uint64"
      #end if 
   </command>
   <inputs>
@@ -107,10 +107,11 @@
         </when>
         <when value="advanced">
             <param name="coverage_dtype" type="select" label="Choose the dtype to use for storing coverage information" help="This affects the maximum recorded value for a position, e.g. uint8 would be 255 coverage, but will require the least amount of RAM">
+                <option value="guess" selected="True">Guess</option>
                 <option value="uint8">uint8</option>
                 <option value="uint16">uint16</option>
                 <option value="uint32">uint32</option>
-                <option value="uint64" selected="True">uint64</option>
+                <option value="uint64">uint64</option>
             </param>
             <param name="safe" type="boolean" truevalue="--safe" falsevalue="" checked="False" label="Be extra safe"/>
         </when>