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); }
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); }
final SAMReadGroupRecord samReadGroupRecord = new SAMReadGroupRecord(parsedHeaderLine.removeValue(SAMReadGroupRecord.READ_GROUP_ID_TAG)); transferAttributes(samReadGroupRecord, parsedHeaderLine.mKeyValuePairs);
final SAMReadGroupRecord samReadGroupRecord = new SAMReadGroupRecord(parsedHeaderLine.removeValue(SAMReadGroupRecord.READ_GROUP_ID_TAG)); transferAttributes(samReadGroupRecord, parsedHeaderLine.mKeyValuePairs);
final SAMReadGroupRecord samReadGroupRecord = new SAMReadGroupRecord(parsedHeaderLine.removeValue(SAMReadGroupRecord.READ_GROUP_ID_TAG)); transferAttributes(samReadGroupRecord, 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); }