# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1362454650 21600
# Node ID 1061731ba6ede4b7c8e684ad2a21fe9b32ee665d
# Parent  dd9f8ea2b718d31b6d14fd883a1a84d1e9b1c2f8
Update options for UnifiedGenotyper p_nonref_model for version 2.3

diff -r dd9f8ea2b718 -r 1061731ba6ed unified_genotyper.xml
--- a/unified_genotyper.xml	Fri Mar 01 12:43:41 2013 -0600
+++ b/unified_genotyper.xml	Mon Mar 04 21:37:30 2013 -0600
@@ -443,8 +443,8 @@
       </when>
       <when value="advanced">
         <param name="p_nonref_model" type="select" label="Non-reference probability calculation model to employ" help="-pnrm,--p_nonref_model &amp;lt;p_nonref_model&amp;gt;">
-          <option value="EXACT" selected="True">EXACT</option>
-          <option value="GRID_SEARCH">GRID_SEARCH</option>
+          <option value="EXACT_GENERAL_PLOIDY" selected="True">EXACT_GENERAL_PLOIDY (supports any sample ploidy)</option>
+          <option value="EXACT_REFERENCE">EXACT_REFERENCE (multi-allelic EXACT model.  Extremely slow for many alternate alleles)</option>
         </param>
         <param name="heterozygosity" type="float" value="1e-3" label="Heterozygosity value used to compute prior likelihoods for any locus" help="-hets,--heterozygosity &amp;lt;heterozygosity&amp;gt;" />
         <param name="pcr_error_rate" type="float" value="1e-4" label="The PCR error rate to be used for computing fragment-based likelihoods" help="-pcr_error,--pcr_error_rate &amp;lt;pcr_error_rate&amp;gt;" />
@@ -598,7 +598,7 @@
 **Settings**::
 
  genotype_likelihoods_model                        Genotype likelihoods calculation model to employ -- BOTH is the default option, while INDEL is also available for calling indels and SNP is available for calling SNPs only (SNP|INDEL|BOTH)
- p_nonref_model                                    Non-reference probability calculation model to employ -- EXACT is the default option, while GRID_SEARCH is also available. (EXACT|GRID_SEARCH)
+ p_nonref_model                                    Non-reference probability calculation model to employ -- EXACT_GENERAL_PLOIDY is the default option, while EXACT_REFERENCE is also available. (EXACT_INDEPENDENT,EXACT_REFERENCE,EXACT_ORIGINAL,EXACT_GENERAL_PLOIDY)
  heterozygosity                                    Heterozygosity value used to compute prior likelihoods for any locus
  pcr_error_rate                                    The PCR error rate to be used for computing fragment-based likelihoods
  genotyping_mode                                   Should we output confident genotypes (i.e. including ref calls) or just the variants? (DISCOVERY|GENOTYPE_GIVEN_ALLELES)