--- 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()