private void validateSamFile(final SAMFileReader samReader, final PrintWriter out) { try { samReader.setValidationStringency(ValidationStringency.SILENT); validateHeader(samReader.getFileHeader()); orderChecker = new SAMSortOrderChecker(samReader.getFileHeader().getSortOrder()); validateSamRecordsAndQualityFormat(samReader, samReader.getFileHeader()); validateUnmatchedPairs(); if (validateIndex) { try { BamIndexValidator.exhaustivelyTestIndex(samReader); } catch (Exception e) { addError(new SAMValidationError(Type.INVALID_INDEX_FILE_POINTER, e.getMessage(), null)); } } if (errorsByType.isEmpty()) { out.println("No errors found"); } } finally { out.flush(); } }
private void validateSamFile(final SamReader samReader, final PrintWriter out) { try { validateHeader(samReader.getFileHeader()); orderChecker = new SAMSortOrderChecker(samReader.getFileHeader().getSortOrder()); validateSamRecordsAndQualityFormat(samReader, samReader.getFileHeader()); validateUnmatchedPairs(); if (indexValidationStringency != IndexValidationStringency.NONE) { try { if (indexValidationStringency == IndexValidationStringency.LESS_EXHAUSTIVE) { BamIndexValidator.lessExhaustivelyTestIndex(samReader); } else { BamIndexValidator.exhaustivelyTestIndex(samReader); } } catch (Exception e) { addError(new SAMValidationError(Type.INVALID_INDEX_FILE_POINTER, e.getMessage(), null)); } } if (errorsByType.isEmpty()) { out.println("No errors found"); } } finally { out.flush(); } }
private void validateSamFile(final SamReader samReader, final PrintWriter out) { try { validateHeader(samReader.getFileHeader()); orderChecker = new SAMSortOrderChecker(samReader.getFileHeader().getSortOrder()); validateSamRecordsAndQualityFormat(samReader, samReader.getFileHeader()); validateUnmatchedPairs(); if (indexValidationStringency != IndexValidationStringency.NONE) { try { if (indexValidationStringency == IndexValidationStringency.LESS_EXHAUSTIVE) { BamIndexValidator.lessExhaustivelyTestIndex(samReader); } else { BamIndexValidator.exhaustivelyTestIndex(samReader); } } catch (Exception e) { addError(new SAMValidationError(Type.INVALID_INDEX_FILE_POINTER, e.getMessage(), null)); } } if (errorsByType.isEmpty()) { out.println("No errors found"); } } finally { out.flush(); } }