private void writePGLine(final SAMProgramRecord programRecord) { println(getPGLine(programRecord)); }
private void writeRGLine(final SAMReadGroupRecord readGroup) { println(getRGLine(readGroup)); }
private void writePGLine(final SAMProgramRecord programRecord) { println(getPGLine(programRecord)); }
private void writeSQLine(final SAMSequenceRecord sequenceRecord) { println(getSQLine(sequenceRecord)); }
private void writeRGLine(final SAMReadGroupRecord readGroup) { println(getRGLine(readGroup)); }
private void writeSQLine(final SAMSequenceRecord sequenceRecord) { println(getSQLine(sequenceRecord)); }
private void writePGLine(final SAMProgramRecord programRecord) { if (programRecord == null) { return; } final String[] fields = new String[2 + programRecord.getAttributes().size()]; fields[0] = HEADER_LINE_START + HeaderRecordType.PG; fields[1] = SAMProgramRecord.PROGRAM_GROUP_ID_TAG + TAG_KEY_VALUE_SEPARATOR + programRecord.getProgramGroupId(); encodeTags(programRecord, fields, 2); println(StringUtil.join(FIELD_SEPARATOR, fields)); }
private void writeRGLine(final SAMReadGroupRecord readGroup) { final String[] fields = new String[2 + readGroup.getAttributes().size()]; fields[0] = HEADER_LINE_START + HeaderRecordType.RG; fields[1] = SAMReadGroupRecord.READ_GROUP_ID_TAG + TAG_KEY_VALUE_SEPARATOR + readGroup.getReadGroupId(); encodeTags(readGroup, fields, 2); println(StringUtil.join(FIELD_SEPARATOR, fields)); }
private void writeHDLine(final boolean keepExistingVersionNumber) { final SAMFileHeader newHeader; if (keepExistingVersionNumber) { newHeader = mFileHeader; } else { // Make a copy of the header, excluding the version from the input header, so that // output get CURRENT_VERSION instead of whatever the version of the input header was. newHeader = new SAMFileHeader(); for (final Map.Entry<String, String> entry : mFileHeader.getAttributes()) { if (!entry.getKey().equals(SAMFileHeader.VERSION_TAG)) { newHeader.setAttribute(entry.getKey(), entry.getValue()); } } } final String[] fields = new String[1 + newHeader.getAttributes().size()]; fields[0] = HEADER_LINE_START + HeaderRecordType.HD; encodeTags(newHeader, fields, 1); println(StringUtil.join(FIELD_SEPARATOR, fields)); }
private void writeHDLine(final boolean keepExistingVersionNumber) { final SAMFileHeader newHeader; if (keepExistingVersionNumber) { newHeader = mFileHeader; } else { // Make a copy of the header, excluding the version from the input header, so that // output get CURRENT_VERSION instead of whatever the version of the input header was. newHeader = new SAMFileHeader(); for (final Map.Entry<String, String> entry : mFileHeader.getAttributes()) { if (!entry.getKey().equals(SAMFileHeader.VERSION_TAG)) { newHeader.setAttribute(entry.getKey(), entry.getValue()); } } } final String[] fields = new String[1 + newHeader.getAttributes().size()]; fields[0] = HEADER_LINE_START + HeaderRecordType.HD; encodeTags(newHeader, fields, 1); println(StringUtil.join(FIELD_SEPARATOR, fields)); }
private void writeHDLine(final boolean keepExistingVersionNumber) { final SAMFileHeader newHeader; if (keepExistingVersionNumber) { newHeader = mFileHeader; } else { // Make a copy of the header, excluding the version from the input header, so that // output get CURRENT_VERSION instead of whatever the version of the input header was. newHeader = new SAMFileHeader(); for (final Map.Entry<String, String> entry : mFileHeader.getAttributes()) { if (!entry.getKey().equals(SAMFileHeader.VERSION_TAG)) { newHeader.setAttribute(entry.getKey(), entry.getValue()); } } } final String[] fields = new String[1 + newHeader.getAttributes().size()]; fields[0] = HEADER_LINE_START + HeaderRecordType.HD; encodeTags(newHeader, fields, 1); println(StringUtil.join(FIELD_SEPARATOR, fields)); }
private void writeSQLine(final SAMSequenceRecord sequenceRecord) { final int numAttributes =sequenceRecord.getAttributes() != null ? sequenceRecord.getAttributes().size() : 0; final String[] fields = new String[3 + numAttributes]; fields[0] = HEADER_LINE_START + HeaderRecordType.SQ; fields[1] = SAMSequenceRecord.SEQUENCE_NAME_TAG + TAG_KEY_VALUE_SEPARATOR + sequenceRecord.getSequenceName(); fields[2] = SAMSequenceRecord.SEQUENCE_LENGTH_TAG + TAG_KEY_VALUE_SEPARATOR + Integer.toString(sequenceRecord.getSequenceLength()); encodeTags(sequenceRecord, fields, 3); println(StringUtil.join(FIELD_SEPARATOR, fields)); }
/** * Convert SAMFileHeader from in-memory representation to text representation. * @param writer where to write the header text. * @param header object to be converted to text. * @param keepExistingVersionNumber If true, writes whatever version # was in the header. If false, writes * SAMFileHeader.CURRENT_VERSION. */ public void encode(final Writer writer, final SAMFileHeader header, final boolean keepExistingVersionNumber) { mFileHeader = header; this.writer = new BufferedWriter(writer); writeHDLine(keepExistingVersionNumber); for (final SAMSequenceRecord sequenceRecord: header.getSequenceDictionary().getSequences()) { writeSQLine(sequenceRecord); } for (final SAMReadGroupRecord readGroup : header.getReadGroups()) { writeRGLine(readGroup); } for (final SAMProgramRecord programRecord : header.getProgramRecords()) { writePGLine(programRecord); } for (final String comment : header.getComments()) { println(comment); } try { this.writer.flush(); } catch (IOException e) { throw new RuntimeIOException(e); } }
/** * Convert SAMFileHeader from in-memory representation to text representation. * @param writer where to write the header text. * @param header object to be converted to text. * @param keepExistingVersionNumber If true, writes whatever version # was in the header. If false, writes * SAMFileHeader.CURRENT_VERSION. */ public void encode(final Writer writer, final SAMFileHeader header, final boolean keepExistingVersionNumber) { mFileHeader = header; this.writer = new BufferedWriter(writer); writeHDLine(keepExistingVersionNumber); for (final SAMSequenceRecord sequenceRecord: header.getSequenceDictionary().getSequences()) { writeSQLine(sequenceRecord); } for (final SAMReadGroupRecord readGroup : header.getReadGroups()) { writeRGLine(readGroup); } for (final SAMProgramRecord programRecord : header.getProgramRecords()) { writePGLine(programRecord); } for (final String comment : header.getComments()) { println(comment); } try { this.writer.flush(); } catch (IOException e) { throw new RuntimeIOException(e); } }
/** * Convert SAMFileHeader from in-memory representation to text representation. * @param writer where to write the header text. * @param header object to be converted to text. * @param keepExistingVersionNumber If true, writes whatever version # was in the header. If false, writes * SAMFileHeader.CURRENT_VERSION. */ public void encode(final Writer writer, final SAMFileHeader header, final boolean keepExistingVersionNumber) { mFileHeader = header; this.writer = new BufferedWriter(writer); writeHDLine(keepExistingVersionNumber); for (final SAMSequenceRecord sequenceRecord: header.getSequenceDictionary().getSequences()) { writeSQLine(sequenceRecord); } for (final SAMReadGroupRecord readGroup : header.getReadGroups()) { writeRGLine(readGroup); } for (final SAMProgramRecord programRecord : header.getProgramRecords()) { writePGLine(programRecord); } for (final String comment : header.getComments()) { println(comment); } try { this.writer.flush(); } catch (IOException e) { throw new RuntimeIOException(e); } }