samReadGroupRecord.setAttribute(SAMReadGroupRecord.PREDICTED_MEDIAN_INSERT_SIZE_TAG,predictedMedianInsertSize); } catch (NumberFormatException e) { reportErrorParsingLine(SAMReadGroupRecord.PREDICTED_MEDIAN_INSERT_SIZE_TAG + " is not numeric: " + predictedMedianInsertSize, SAMValidationError.Type.INVALID_PREDICTED_MEDIAN_INSERT_SIZE, e); reportErrorParsingLine(SAMReadGroupRecord.DATE_RUN_PRODUCED_TAG + " tag value '" + dateRunProduced + "' is not parseable as a date", SAMValidationError.Type.INVALID_DATE_STRING, e);
private void parseHDLine(final ParsedHeaderLine parsedHeaderLine) { assert(HeaderRecordType.HD.equals(parsedHeaderLine.getHeaderRecordType())); if (!parsedHeaderLine.requireTag(SAMFileHeader.VERSION_TAG)) { return; } final String soString = parsedHeaderLine.getValue(SAMFileHeader.SORT_ORDER_TAG); try { if (soString != null) SortOrder.valueOf(soString); } catch (IllegalArgumentException e) { reportErrorParsingLine(HEADER_LINE_START + parsedHeaderLine.getHeaderRecordType() + " line has non-conforming SO tag value: " + soString + ".", SAMValidationError.Type.HEADER_TAG_NON_CONFORMING_VALUE, null); } final String goString = parsedHeaderLine.getValue(SAMFileHeader.GROUP_ORDER_TAG); try { if (goString != null) SAMFileHeader.GroupOrder.valueOf(goString); } catch (IllegalArgumentException e) { reportErrorParsingLine(HEADER_LINE_START + parsedHeaderLine.getHeaderRecordType() + " line has non-conforming GO tag value: "+ goString + ".", SAMValidationError.Type.HEADER_TAG_NON_CONFORMING_VALUE, null); } transferAttributes(mFileHeader, parsedHeaderLine.mKeyValuePairs); }
samReadGroupRecord.setAttribute(SAMReadGroupRecord.PREDICTED_MEDIAN_INSERT_SIZE_TAG,predictedMedianInsertSize); } catch (NumberFormatException e) { reportErrorParsingLine(SAMReadGroupRecord.PREDICTED_MEDIAN_INSERT_SIZE_TAG + " is not numeric: " + predictedMedianInsertSize, SAMValidationError.Type.INVALID_PREDICTED_MEDIAN_INSERT_SIZE, e); reportErrorParsingLine(SAMReadGroupRecord.DATE_RUN_PRODUCED_TAG + " tag value '" + dateRunProduced + "' is not parseable as a date", SAMValidationError.Type.INVALID_DATE_STRING, e);
samReadGroupRecord.setAttribute(SAMReadGroupRecord.PREDICTED_MEDIAN_INSERT_SIZE_TAG,predictedMedianInsertSize); } catch (NumberFormatException e) { reportErrorParsingLine(SAMReadGroupRecord.PREDICTED_MEDIAN_INSERT_SIZE_TAG + " is not numeric: " + predictedMedianInsertSize, SAMValidationError.Type.INVALID_PREDICTED_MEDIAN_INSERT_SIZE, e); reportErrorParsingLine(SAMReadGroupRecord.DATE_RUN_PRODUCED_TAG + " tag value '" + dateRunProduced + "' is not parseable as a date", SAMValidationError.Type.INVALID_DATE_STRING, e);
private void parseHDLine(final ParsedHeaderLine parsedHeaderLine) { assert(HeaderRecordType.HD.equals(parsedHeaderLine.getHeaderRecordType())); if (!parsedHeaderLine.requireTag(SAMFileHeader.VERSION_TAG)) { return; } final String soString = parsedHeaderLine.getValue(SAMFileHeader.SORT_ORDER_TAG); try { if (soString != null) SortOrder.valueOf(soString); } catch (IllegalArgumentException e) { reportErrorParsingLine(HEADER_LINE_START + parsedHeaderLine.getHeaderRecordType() + " line has non-conforming SO tag value: " + soString + ".", SAMValidationError.Type.HEADER_TAG_NON_CONFORMING_VALUE, null); } final String goString = parsedHeaderLine.getValue(SAMFileHeader.GROUP_ORDER_TAG); try { if (goString != null) SAMFileHeader.GroupOrder.valueOf(goString); } catch (IllegalArgumentException e) { reportErrorParsingLine(HEADER_LINE_START + parsedHeaderLine.getHeaderRecordType() + " line has non-conforming GO tag value: "+ goString + ".", SAMValidationError.Type.HEADER_TAG_NON_CONFORMING_VALUE, null); } transferAttributes(mFileHeader, parsedHeaderLine.mKeyValuePairs); }