/** * Handle a list of validation errors according to the validation stringency. * @param validationErrors List of errors to report, or null if there are no errors. * @param samRecordIndex Record number of the SAMRecord corresponding to the validation errors, or -1 if * the record number is not known. * @param validationStringency If STRICT, throw a SAMFormatException. If LENIENT, print the validation * errors to stderr. If SILENT, do nothing. */ static void processValidationErrors(final List<SAMValidationError> validationErrors, final long samRecordIndex, final ValidationStringency validationStringency) { if (validationErrors != null && validationErrors.size() > 0) { for (final SAMValidationError validationError : validationErrors) { validationError.setRecordNumber(samRecordIndex); } if (validationStringency == ValidationStringency.STRICT) { throw new SAMFormatException("SAM validation error: " + validationErrors.get(0)); } else if (validationStringency == ValidationStringency.LENIENT) { for (final SAMValidationError error : validationErrors) { System.err.println("Ignoring SAM validation error: " + error); } } } }
/** * Handle a list of validation errors according to the validation stringency. * * @param validationErrors List of errors to report, or null if there are no errors. * @param samRecordIndex Record number of the SAMRecord corresponding to the validation errors, or -1 if * the record number is not known. * @param validationStringency If STRICT, throw a SAMFormatException. If LENIENT, print the validation * errors to stderr. If SILENT, do nothing. */ public static void processValidationErrors(final List<SAMValidationError> validationErrors, final long samRecordIndex, final ValidationStringency validationStringency) { if (validationErrors != null && !validationErrors.isEmpty()) { for (final SAMValidationError validationError : validationErrors) { validationError.setRecordNumber(samRecordIndex); } if (validationStringency == ValidationStringency.STRICT) { throw new SAMFormatException("SAM validation error: " + validationErrors.get(0)); } else if (validationStringency == ValidationStringency.LENIENT) { for (final SAMValidationError error : validationErrors) { System.err.println("Ignoring SAM validation error: " + error); } } } }
/** * Handle a list of validation errors according to the validation stringency. * * @param validationErrors List of errors to report, or null if there are no errors. * @param samRecordIndex Record number of the SAMRecord corresponding to the validation errors, or -1 if * the record number is not known. * @param validationStringency If STRICT, throw a SAMFormatException. If LENIENT, print the validation * errors to stderr. If SILENT, do nothing. */ public static void processValidationErrors(final List<SAMValidationError> validationErrors, final long samRecordIndex, final ValidationStringency validationStringency) { if (validationErrors != null && !validationErrors.isEmpty()) { for (final SAMValidationError validationError : validationErrors) { validationError.setRecordNumber(samRecordIndex); } if (validationStringency == ValidationStringency.STRICT) { throw new SAMFormatException("SAM validation error: " + validationErrors.get(0)); } else if (validationStringency == ValidationStringency.LENIENT) { for (final SAMValidationError error : validationErrors) { System.err.println("Ignoring SAM validation error: " + error); } } } }
/** * Handle a list of validation errors according to the validation stringency. * * @param validationErrors List of errors to report, or null if there are no errors. * @param samRecordIndex Record number of the SAMRecord corresponding to the validation errors, or -1 if * the record number is not known. * @param validationStringency If STRICT, throw a SAMFormatException. If LENIENT, print the validation * errors to stderr. If SILENT, do nothing. */ public static void processValidationErrors(final List<SAMValidationError> validationErrors, final long samRecordIndex, final ValidationStringency validationStringency) { if (validationErrors != null && !validationErrors.isEmpty()) { for (final SAMValidationError validationError : validationErrors) { validationError.setRecordNumber(samRecordIndex); } if (validationStringency == ValidationStringency.STRICT) { throw new SAMFormatException("SAM validation error: " + validationErrors.get(0)); } else if (validationStringency == ValidationStringency.LENIENT) { for (final SAMValidationError error : validationErrors) { System.err.println("Ignoring SAM validation error: " + error); } } } }
if (errors != null) { for (final SAMValidationError error : errors) { error.setRecordNumber(recordNumber); addError(error);
if (errors != null) { for (final SAMValidationError error : errors) { error.setRecordNumber(recordNumber); addError(error);
if (errors != null) { for (final SAMValidationError error : errors) { error.setRecordNumber(recordNumber); addError(error);