# HG changeset patch
# User Daniel Blankenberg <dan@bx.psu.edu>
# Date 1391552786 18000
# Node ID 8398666758e37c63c578f7b3ebb44bfdf656a03e
# Parent  13d534f2bcde97f3c8ef65d5130fea18a7969640
Update options.

diff -r 13d534f2bcde -r 8398666758e3 dependency_configs/tool_dependencies.xml
--- a/dependency_configs/tool_dependencies.xml	Mon Sep 16 10:41:15 2013 -0400
+++ b/dependency_configs/tool_dependencies.xml	Tue Feb 04 17:26:26 2014 -0500
@@ -1,11 +1,11 @@
 <tool_dependency>
     <package name="numpy" version="1.7.1">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_numpy_1_7" owner="iuc" changeset_revision="74c21f9bdc39" />
+        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_numpy_1_7" owner="iuc" changeset_revision="ef12a3a11d5b" />
     </package>
     <package name="pyBamParser" version="0.0.1">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_pybamparser_0_0_1" owner="blankenberg" changeset_revision="ae1828dd8bbc" />
+        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_pybamparser_0_0_1" owner="blankenberg" changeset_revision="0b2c2790838a" />
     </package>
     <package name="pyBamTools" version="0.0.1">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_pybamtools_0_0_1" owner="blankenberg" changeset_revision="de60d1631ce4" />
+        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_pybamtools_0_0_1" owner="blankenberg" changeset_revision="b97259dc9149" />
     </package>
 </tool_dependency>
diff -r 13d534f2bcde -r 8398666758e3 tools/naive_variant_caller.py
--- a/tools/naive_variant_caller.py	Mon Sep 16 10:41:15 2013 -0400
+++ b/tools/naive_variant_caller.py	Tue Feb 04 17:26:26 2014 -0500
@@ -18,8 +18,9 @@
     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='uint8', help='dtype to use for coverage array' )
+    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( '--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' )
     (options, args) = parser.parse_args()
     
@@ -55,8 +56,9 @@
             regions.append( region )
     
     coverage = VCFReadGroupGenotyper( map( lambda x: Reader( *x ), bam_files ), options.reference_genome_filename, dtype=options.coverage_dtype,
-                                               min_support_depth=options.min_support_depth, min_base_quality=options.min_base_quality, min_mapping_quality=options.min_mapping_quality,
-                                               restrict_regions=regions, use_strand=options.use_strand, allow_out_of_bounds_positions=options.allow_out_of_bounds_positions )
+                                               min_support_depth=options.min_support_depth, min_base_quality=options.min_base_quality, 
+                                               min_mapping_quality=options.min_mapping_quality, restrict_regions=regions, use_strand=options.use_strand, 
+                                               allow_out_of_bounds_positions=options.allow_out_of_bounds_positions, safe=options.safe )
     for line in coverage.iter_vcf( ploidy=options.ploidy, variants_only=options.variants_only ):
         out.write( "%s\n" % line )
     out.close()
diff -r 13d534f2bcde -r 8398666758e3 tools/naive_variant_caller.xml
--- a/tools/naive_variant_caller.xml	Mon Sep 16 10:41:15 2013 -0400
+++ b/tools/naive_variant_caller.xml	Tue Feb 04 17:26:26 2014 -0500
@@ -43,10 +43,14 @@
          --min_mapping_quality "${min_mapping_quality}"
      #end if
      
-     --coverage_dtype "${coverage_dtype}"
-     
      --allow_out_of_bounds_positions
      
+     #if str( $advanced_options.advanced_options_selector ) == "advanced":
+         --coverage_dtype "${advanced_options.coverage_dtype}"
+         ${advanced_options.safe}
+     #else
+         --coverage_dtype "uint64"
+     #end if 
   </command>
   <inputs>
     <conditional name="reference_source">
@@ -93,12 +97,24 @@
     
     <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="False" label="Report counts by strand"/>
     
-    <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="uint8">uint8</option>
-      <option value="uint16" selected="True">uint16</option>
-      <option value="uint32">uint32</option>
-      <option value="uint64">uint64</option>
-    </param>
+    <conditional name="advanced_options">
+        <param name="advanced_options_selector" type="select" label="Show Advanced Options">
+            <option value="basic" selected="True">Hide Advanced Options</option>
+            <option value="advanced">Show Advanced Options</option>
+        </param>
+        <when value="basic">
+            <!-- Do nothing here -->
+        </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="uint8">uint8</option>
+                <option value="uint16">uint16</option>
+                <option value="uint32">uint32</option>
+                <option value="uint64" selected="True">uint64</option>
+            </param>
+            <param name="safe" type="boolean" truevalue="--safe" falsevalue="" checked="False" label="Be extra safe"/>
+        </when>
+    </conditional>
     
   </inputs>
   <outputs>
@@ -200,6 +216,7 @@
           <param name="ploidy" value="2" />
           <param name="variants_only" value="False" />
           <param name="use_strand" value="False" />
+          <param name="advanced_options_selector" value="advanced" />
           <param name="coverage_dtype" value="uint8" />
           <output name="output_vcf" file="fake_phiX174_reads_1_test_out_1.vcf" compare="contains" />
       </test>