private void parseSQLine(final ParsedHeaderLine parsedHeaderLine) { assert(HeaderRecordType.SQ.equals(parsedHeaderLine.getHeaderRecordType())); if (!parsedHeaderLine.requireTag(SAMSequenceRecord.SEQUENCE_NAME_TAG) || !parsedHeaderLine.requireTag(SAMSequenceRecord.SEQUENCE_LENGTH_TAG)) { return; } String sequenceName = parsedHeaderLine.removeValue(SAMSequenceRecord.SEQUENCE_NAME_TAG); sequenceName = SAMSequenceRecord.truncateSequenceName(sequenceName); final SAMSequenceRecord samSequenceRecord = new SAMSequenceRecord(sequenceName, Integer.parseInt(parsedHeaderLine.removeValue(SAMSequenceRecord.SEQUENCE_LENGTH_TAG))); transferAttributes(samSequenceRecord, parsedHeaderLine.mKeyValuePairs); sequences.add(samSequenceRecord); }
mHeaderRecordType = HeaderRecordType.valueOf(fields[0].substring(1)); } catch (IllegalArgumentException e) { reportErrorParsingLine("Unrecognized header record type", SAMValidationError.Type.UNRECOGNIZED_HEADER_TYPE, null);
mHeaderRecordType = HeaderRecordType.valueOf(fields[0].substring(1)); } catch (IllegalArgumentException e) { reportErrorParsingLine("Unrecognized header record type", SAMValidationError.Type.UNRECOGNIZED_HEADER_TYPE, null);
private void parseRGLine(final ParsedHeaderLine parsedHeaderLine) { assert(HeaderRecordType.RG.equals(parsedHeaderLine.getHeaderRecordType())); if (!parsedHeaderLine.requireTag(SAMReadGroupRecord.READ_GROUP_ID_TAG)) { return;
private void parseRGLine(final ParsedHeaderLine parsedHeaderLine) { assert(HeaderRecordType.RG.equals(parsedHeaderLine.getHeaderRecordType())); if (!parsedHeaderLine.requireTag(SAMReadGroupRecord.READ_GROUP_ID_TAG)) { return;
mHeaderRecordType = HeaderRecordType.valueOf(fields[0].substring(1)); } catch (IllegalArgumentException e) { reportErrorParsingLine("Unrecognized header record type", SAMValidationError.Type.UNRECOGNIZED_HEADER_TYPE, null);
private void parseRGLine(final ParsedHeaderLine parsedHeaderLine) { assert(HeaderRecordType.RG.equals(parsedHeaderLine.getHeaderRecordType())); if (!parsedHeaderLine.requireTag(SAMReadGroupRecord.READ_GROUP_ID_TAG)) { return;
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); }
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); }
private void parseHDLine(final ParsedHeaderLine parsedHeaderLine) { assert(HeaderRecordType.HD.equals(parsedHeaderLine.getHeaderRecordType())); if (!parsedHeaderLine.requireTag(SAMFileHeader.VERSION_TAG)) { return; } transferAttributes(mFileHeader, parsedHeaderLine.mKeyValuePairs); }
private void parsePGLine(final ParsedHeaderLine parsedHeaderLine) { assert(HeaderRecordType.PG.equals(parsedHeaderLine.getHeaderRecordType())); if (!parsedHeaderLine.requireTag(SAMProgramRecord.PROGRAM_GROUP_ID_TAG)) { return; } final SAMProgramRecord programRecord = new SAMProgramRecord(parsedHeaderLine.removeValue(SAMProgramRecord.PROGRAM_GROUP_ID_TAG)); transferAttributes(programRecord, parsedHeaderLine.mKeyValuePairs); mFileHeader.addProgramRecord(programRecord); }
private void parsePGLine(final ParsedHeaderLine parsedHeaderLine) { assert(HeaderRecordType.PG.equals(parsedHeaderLine.getHeaderRecordType())); if (!parsedHeaderLine.requireTag(SAMProgramRecord.PROGRAM_GROUP_ID_TAG)) { return; } final SAMProgramRecord programRecord = new SAMProgramRecord(parsedHeaderLine.removeValue(SAMProgramRecord.PROGRAM_GROUP_ID_TAG)); transferAttributes(programRecord, parsedHeaderLine.mKeyValuePairs); mFileHeader.addProgramRecord(programRecord); }
private void parsePGLine(final ParsedHeaderLine parsedHeaderLine) { assert(HeaderRecordType.PG.equals(parsedHeaderLine.getHeaderRecordType())); if (!parsedHeaderLine.requireTag(SAMProgramRecord.PROGRAM_GROUP_ID_TAG)) { return; } final SAMProgramRecord programRecord = new SAMProgramRecord(parsedHeaderLine.removeValue(SAMProgramRecord.PROGRAM_GROUP_ID_TAG)); transferAttributes(programRecord, parsedHeaderLine.mKeyValuePairs); mFileHeader.addProgramRecord(programRecord); }
private void parseSQLine(final ParsedHeaderLine parsedHeaderLine) { assert(HeaderRecordType.SQ.equals(parsedHeaderLine.getHeaderRecordType())); if (!parsedHeaderLine.requireTag(SAMSequenceRecord.SEQUENCE_NAME_TAG) || !parsedHeaderLine.requireTag(SAMSequenceRecord.SEQUENCE_LENGTH_TAG)) { return; } String sequenceName = parsedHeaderLine.removeValue(SAMSequenceRecord.SEQUENCE_NAME_TAG); sequenceName = SAMSequenceRecord.truncateSequenceName(sequenceName); final SAMSequenceRecord samSequenceRecord = new SAMSequenceRecord(sequenceName, Integer.parseInt(parsedHeaderLine.removeValue(SAMSequenceRecord.SEQUENCE_LENGTH_TAG))); transferAttributes(samSequenceRecord, parsedHeaderLine.mKeyValuePairs); sequences.add(samSequenceRecord); }
private void parseSQLine(final ParsedHeaderLine parsedHeaderLine) { assert(HeaderRecordType.SQ.equals(parsedHeaderLine.getHeaderRecordType())); if (!parsedHeaderLine.requireTag(SAMSequenceRecord.SEQUENCE_NAME_TAG) || !parsedHeaderLine.requireTag(SAMSequenceRecord.SEQUENCE_LENGTH_TAG)) { return; } String sequenceName = parsedHeaderLine.removeValue(SAMSequenceRecord.SEQUENCE_NAME_TAG); sequenceName = SAMSequenceRecord.truncateSequenceName(sequenceName); final SAMSequenceRecord samSequenceRecord = new SAMSequenceRecord(sequenceName, Integer.parseInt(parsedHeaderLine.removeValue(SAMSequenceRecord.SEQUENCE_LENGTH_TAG))); transferAttributes(samSequenceRecord, parsedHeaderLine.mKeyValuePairs); sequences.add(samSequenceRecord); }