Examples of net.sf.samtools.util.RuntimeIOException

net.sf.samtools.util.RuntimeIOException
Thrown by various IO classes to indicate IOException without having to clutter the API with throws clauses

                throw new SAMFormatException("Unrecognized file format: " + strm);
            }
            setValidationStringency(validationStringency);
        }
        catch (IOException e) {
            throw new RuntimeIOException(e);
        }
    }

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            setValidationStringency(validationStringency);
            mReader.setSAMRecordFactory(this.samRecordFactory);
        }
        catch (IOException e) {
            throw new RuntimeIOException(e);
        }
    }

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        FeatureFileFormat featureFileFormat = DocumentUtils.guessFeaturesFileFormat(featureFile);


        if (featureFileFormat == FeatureFileFormat.UNKNOWN) {
            throw new RuntimeIOException("Unknown feature file format. Please provide file in GFF/GTF or BED format.");
        }


        if (featureFileFormat == FeatureFileFormat.GTF) {
            // while not interested in GTF-specific information we save some memory by using GFF reader
            featureFileFormat = FeatureFileFormat.GFF;

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Related Classes of net.sf.samtools.util.RuntimeIOException

net.sf.samtools.SAMFileReader

org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis

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