Examples of org.broadinstitute.gatk.utils.exceptions.GATKException

Package org.broadinstitute.gatk.utils.exceptions

Examples of org.broadinstitute.gatk.utils.exceptions.GATKException

org.broadinstitute.gatk.utils.exceptions.GATKException
@author aaron @version 1.0 @date Apr 6, 2009
Class GATKException
This exception allows us to filter out exceptions that come from core GATK code, and those that are not homegrown..

    private void closeInputStream(final FileInputStream inputStream) {
        try {
            inputStream.close();
        }
        catch(IOException ex) {
            throw new GATKException("Unable to open input file");
        }
    }

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        File indexFile = Tribble.indexFile(resultFile);
        //System.out.println("Putative index file is " + indexFile);
        if ( indexFile.exists() ) {
            if ( resultFile.getAbsolutePath().contains(".vcf") ) {
                // todo -- currently we only understand VCF files! Blow up since we can't test them
                throw new GATKException("Found an index created for file " + resultFile + " but we can only validate VCF files.  Extend this code!");
            }


            System.out.println("Verifying on-the-fly index " + indexFile + " for test " + name + " using file " + resultFile);
            Index indexFromOutputFile = IndexFactory.createDynamicIndex(resultFile, new VCFCodec());
            Index dynamicIndex = IndexFactory.loadIndex(indexFile.getAbsolutePath());

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        for (String name : sampleNameList) {
            try {
                samples.add(getSample(name));
            }
            catch (Exception e) {
                throw new GATKException("Could not get sample with the following ID: " + name, e);
            }
        }
        return samples;
    }

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            }


            return sampleContamination;


        } catch (IOException e) {
            throw new GATKException("I/O Error while reading sample-contamination file " + ContaminationFractionFile.getName() + ": " + e.getMessage());
        }


    }

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            } else if ( otherGenotypes != null && otherGenotypes.containsSample(sample) ) {
                genotype = otherGenotypes.get(sample);
                isValidation = ! isValidationSite;
            } else {
                // there is magically no genotype for this sample.
                throw new GATKException("Sample "+sample+" arose with no genotype in variant or validation VCF. This should never happen.");
            }


            /*
             * Use likelihoods if: is validation, prior is negative; or: is not validation, has genotype key
             */

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                    vs.setVariantEvalWalker(variantEvalWalker);
                    vs.initialize();


                    strats.add(vs);
                } catch (InstantiationException e) {
                    throw new GATKException("Unable to instantiate stratification module '" + c.getSimpleName() + "'");
                } catch (IllegalAccessException e) {
                    throw new GATKException("Illegal access error when trying to instantiate stratification module '" + c.getSimpleName() + "'");
                }
            }
        }


        return new ArrayList<VariantStratifier>(strats);

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                        // this is an atomic value, add a column for it
                        final String format = field.getValue().format();
                        table.addColumn(field.getKey().getName(), format);
                    } catch (SecurityException e) {
                        throw new GATKException("SecurityException: " + e);
                    }
                }
            }
        }

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        super.initialize();    //To change body of overridden methods use File | Settings | File Templates.
        uncachedRef = getToolkit().getReferenceDataSource().getReference();
    }


    private final void throwError(ReferenceContext ref, String message) {
        throw new GATKException(String.format("Site %s failed: %s", ref.getLocus(), message));
    }

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                        bread.append('-');
                        match.append('D');
                    }
                    break;
                default:
                    throw new GATKException("Unexpected Cigar element:" + e.getOperator());
            }
        }
        for ( ; i < ref.length; i++ ) bref.append((char)ref[i]);
        for ( ; j < read.length; j++ ) bread.append((char)read[j]);

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        } else if (type instanceof WildcardType) {
            throw new RuntimeException("We don't support wildcards in arguments: " + type);
        } else if (type instanceof Class<?>) {
            return ((Class) type).getSimpleName();
        } else {
            throw new GATKException("Unknown type: " + type);
        }
    }

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