List of userFriendlyListOfAvailableFeatures() Examples

Examples of userFriendlyListOfAvailableFeatures()

org.broadinstitute.gatk.engine.refdata.tracks.FeatureManager.userFriendlyListOfAvailableFeatures()
Returns a list of the available tribble track names (vcf,dbsnp,etc) that we can load @return

Examples of org.broadinstitute.gatk.engine.refdata.tracks.FeatureManager.userFriendlyListOfAvailableFeatures()

            // validate triplet type
            FeatureManager.FeatureDescriptor descriptor = builderForValidation.getByTriplet(triplet);
            if ( descriptor == null )
                throw new UserException.UnknownTribbleType(rodBinding.getTribbleType(),
                        String.format("Field %s had provided type %s but there's no such Tribble type.  The compatible types are: %n%s",
                                rodBinding.getName(), rodBinding.getTribbleType(), builderForValidation.userFriendlyListOfAvailableFeatures(rodBinding.getType())));
            if ( ! rodBinding.getType().isAssignableFrom(descriptor.getFeatureClass()) )
                throw new UserException.BadArgumentValue(rodBinding.getName(),
                        String.format("Field %s expects Features of type %s, but the input file produces Features of type %s. The compatible types are: %n%s",
                                rodBinding.getName(), rodBinding.getType().getSimpleName(), descriptor.getSimpleFeatureName(),
                                builderForValidation.userFriendlyListOfAvailableFeatures(rodBinding.getType())));

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Examples of org.broadinstitute.gatk.engine.refdata.tracks.FeatureManager.userFriendlyListOfAvailableFeatures()

                                rodBinding.getName(), rodBinding.getTribbleType(), builderForValidation.userFriendlyListOfAvailableFeatures(rodBinding.getType())));
            if ( ! rodBinding.getType().isAssignableFrom(descriptor.getFeatureClass()) )
                throw new UserException.BadArgumentValue(rodBinding.getName(),
                        String.format("Field %s expects Features of type %s, but the input file produces Features of type %s. The compatible types are: %n%s",
                                rodBinding.getName(), rodBinding.getType().getSimpleName(), descriptor.getSimpleFeatureName(),
                                builderForValidation.userFriendlyListOfAvailableFeatures(rodBinding.getType())));




            rodBindings.add(triplet);
        }

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Examples of org.broadinstitute.gatk.engine.refdata.tracks.FeatureManager.userFriendlyListOfAvailableFeatures()

                if ( manager.getByName(tribbleType) == null )
                    throw new UserException.UnknownTribbleType(
                            tribbleType,
                            String.format("Unable to find tribble type '%s' provided on the command line. " +
                                    "Please select a correct type from among the supported types:%n%s",
                                    tribbleType, manager.userFriendlyListOfAvailableFeatures(parameterType)));


            } else {
                // case with 0 or 1 positional tags
                FeatureManager manager = new FeatureManager();

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Examples of org.broadinstitute.gatk.engine.refdata.tracks.FeatureManager.userFriendlyListOfAvailableFeatures()

                            throw new UserException.CouldNotReadInputFile(file, "file could not be read");
                        } else {
                            throw new UserException.CommandLineException(
                                    String.format("No tribble type was provided on the command line and the type of the file could not be determined dynamically. " +
                                            "Please add an explicit type tag :NAME listing the correct type from among the supported types:%n%s",
                                            manager.userFriendlyListOfAvailableFeatures(parameterType)));
                        }
                    }
                }
            }

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