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)); }
List<String> comments = new LinkedList<>(); for(Map.Entry<String, String> entry : samHeader.getAttributes()) { attributes.put(entry.getKey(), entry.getValue());
public static SAMFileHeader duplicateSAMFileHeader(SAMFileHeader toCopy) { SAMFileHeader copy = new SAMFileHeader(); copy.setSortOrder(toCopy.getSortOrder()); copy.setGroupOrder(toCopy.getGroupOrder()); copy.setProgramRecords(toCopy.getProgramRecords()); copy.setReadGroups(toCopy.getReadGroups()); copy.setSequenceDictionary(toCopy.getSequenceDictionary()); for (Map.Entry<String, String> e : toCopy.getAttributes()) copy.setAttribute(e.getKey(), e.getValue()); return copy; }