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comparison base_recalibrator.xml @ 23:2f9bf8bf42b7 draft

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Replace covariate DinucCovariate with ContextCovariate
author Jim Johnson <jj@umn.edu>
date Fri, 28 Dec 2012 12:34:05 -0600
parents bc18c5ad280f
children 6460f2ba6a60
comparison
equal deleted inserted replaced
22:bc18c5ad280f 23:2f9bf8bf42b7
171 <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" help="-cov,--covariate &amp;lt;covariate&amp;gt;" > 171 <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" help="-cov,--covariate &amp;lt;covariate&amp;gt;" >
172 <!-- might we want to load the available covariates from an external configuration file, since additional ones can be added to local installs? --> 172 <!-- might we want to load the available covariates from an external configuration file, since additional ones can be added to local installs? -->
173 <option value="ReadGroupCovariate" /> 173 <option value="ReadGroupCovariate" />
174 <option value="QualityScoreCovariate" /> 174 <option value="QualityScoreCovariate" />
175 <option value="CycleCovariate" /> 175 <option value="CycleCovariate" />
176 <option value="DinucCovariate" /> 176 <option value="ContextCovariate" />
177 <!-- covariates below were pulled from list option --> 177 <!-- covariates below were pulled from list option -->
178 <option value="HomopolymerCovariate" /> 178 <option value="HomopolymerCovariate" />
179 <option value="GCContentCovariate" /> 179 <option value="GCContentCovariate" />
180 <option value="MappingQualityCovariate" /> 180 <option value="MappingQualityCovariate" />
181 <option value="MinimumNQSCovariate" /> 181 <option value="MinimumNQSCovariate" />