public String getVersion() { return getAttribute(VERSION_TAG); }
public String getCreator() { return getAttribute("CR"); }
public String getCreator() { return (String) getAttribute("CR"); }
public String getVersion() { return getAttribute(VERSION_TAG); }
public String getVersion() { return (String) getAttribute("VN"); }
public String getCreator() { return getAttribute("CR"); }
public GroupOrder getGroupOrder() { if (getAttribute("GO") == null) { return GroupOrder.none; } return GroupOrder.valueOf((String)getAttribute("GO")); }
public SortOrder getSortOrder() { final String so = getAttribute("SO"); if (so == null || so.equals("unknown")) { return SortOrder.unsorted; } return SortOrder.valueOf((String) so); }
public GroupOrder getGroupOrder() { if (groupOrder == null) { final String go = getAttribute(GROUP_ORDER_TAG); if (go == null) { groupOrder = GroupOrder.none; } else { try { return GroupOrder.valueOf(go); } catch (IllegalArgumentException e) { log.warn("Found non conforming header GO tag: " + go + ". Treating as 'none'."); groupOrder = GroupOrder.none; } } } return groupOrder; }
public GroupOrder getGroupOrder() { if (groupOrder == null) { final String go = getAttribute(GROUP_ORDER_TAG); if (go == null) { groupOrder = GroupOrder.none; } else { try { return GroupOrder.valueOf(go); } catch (IllegalArgumentException e) { log.warn("Found non conforming header GO tag: " + go + ". Treating as 'none'."); groupOrder = GroupOrder.none; } } } return groupOrder; }
public SortOrder getSortOrder() { if (sortOrder == null) { final String so = getAttribute(SORT_ORDER_TAG); if (so == null) { sortOrder = SortOrder.unsorted; } else { try { return SortOrder.valueOf(so); } catch (IllegalArgumentException e) { log.warn("Found non-conforming header SO tag: " + so + ". Treating as 'unknown'."); sortOrder = SortOrder.unknown; } } } return sortOrder; }
public SortOrder getSortOrder() { if (sortOrder == null) { final String so = getAttribute(SORT_ORDER_TAG); if (so == null) { sortOrder = SortOrder.unsorted; } else { try { return SortOrder.valueOf(so); } catch (IllegalArgumentException e) { log.warn("Found non-conforming header SO tag: " + so + ". Treating as 'unknown'."); sortOrder = SortOrder.unknown; } } } return sortOrder; }
private boolean compareHeaders(SAMFileHeader h1, SAMFileHeader h2) throws Exception { boolean ret = true; if (!options.ignoreFileFormatVersion) { ret = compareValues(h1.getVersion(), h2.getVersion(), "File format version") && ret; } ret = compareValues(h1.getCreator(), h2.getCreator(), "File creator") && ret; ret = compareValues(h1.getAttribute("SO"), h2.getAttribute("SO"), "Sort order") && ret; if (!compareSequenceDictionaries(h1, h2)) { return false; } ret = compareReadGroups(h1, h2) && ret; ret = compareProgramRecords(h1, h2) && ret; return ret; }
private boolean compareHeaders(SAMFileHeader h1, SAMFileHeader h2) throws Exception { boolean ret = true; if (!options.ignoreFileFormatVersion) { ret = compareValues(h1.getVersion(), h2.getVersion(), "File format version") && ret; } ret = compareValues(h1.getCreator(), h2.getCreator(), "File creator") && ret; ret = compareValues(h1.getAttribute("SO"), h2.getAttribute("SO"), "Sort order") && ret; if (!compareSequenceDictionaries(h1, h2)) { return false; } ret = compareReadGroups(h1, h2) && ret; ret = compareProgramRecords(h1, h2) && ret; return ret; }
@Test public void testGroupOrder() { final SAMFileHeader header = new SAMFileHeader(); header.setGroupOrder(SAMFileHeader.GroupOrder.query); Assert.assertEquals(header.getGroupOrder(), SAMFileHeader.GroupOrder.query); Assert.assertEquals(header.getAttribute(SAMFileHeader.GROUP_ORDER_TAG), SAMFileHeader.GroupOrder.query.name()); header.setAttribute(SAMFileHeader.GROUP_ORDER_TAG, SAMFileHeader.GroupOrder.reference.name()); Assert.assertEquals(header.getGroupOrder(), SAMFileHeader.GroupOrder.reference); Assert.assertEquals(header.getAttribute(SAMFileHeader.GROUP_ORDER_TAG), SAMFileHeader.GroupOrder.reference.name()); header.setAttribute(SAMFileHeader.GROUP_ORDER_TAG, SAMFileHeader.GroupOrder.query); Assert.assertEquals(header.getGroupOrder(), SAMFileHeader.GroupOrder.query); Assert.assertEquals(header.getAttribute(SAMFileHeader.GROUP_ORDER_TAG), SAMFileHeader.GroupOrder.query.name()); }
private boolean compareHeaders() { final SAMFileHeader h1 = samReaders[0].getFileHeader(); final SAMFileHeader h2 = samReaders[1].getFileHeader(); boolean ret = compareValues(h1.getVersion(), h2.getVersion(), "File format version"); ret = compareValues(h1.getCreator(), h2.getCreator(), "File creator") && ret; ret = compareValues(h1.getAttribute("SO"), h2.getAttribute("SO"), "Sort order") && ret; if (!compareSequenceDictionaries(h1, h2)) { ret = false; sequenceDictionariesDiffer = true; } ret = compareReadGroups(h1, h2) && ret; ret = compareProgramRecords(h1, h2) && ret; return ret; }
private boolean compareHeaders() { final SAMFileHeader h1 = samReaders[0].getFileHeader(); final SAMFileHeader h2 = samReaders[1].getFileHeader(); boolean ret = compareValues(h1.getVersion(), h2.getVersion(), "File format version"); ret = compareValues(h1.getCreator(), h2.getCreator(), "File creator") && ret; ret = compareValues(h1.getAttribute("SO"), h2.getAttribute("SO"), "Sort order") && ret; if (!compareSequenceDictionaries(h1, h2)) { ret = false; sequenceDictionariesDiffer = true; } ret = compareReadGroups(h1, h2) && ret; ret = compareProgramRecords(h1, h2) && ret; return ret; }
@Test public void testSortOrderManualSetting() { final SAMFileHeader header = new SAMFileHeader(); header.setSortOrder(SAMFileHeader.SortOrder.coordinate); Assert.assertEquals(header.getSortOrder(), SAMFileHeader.SortOrder.coordinate); Assert.assertEquals(header.getAttribute(SAMFileHeader.SORT_ORDER_TAG), SAMFileHeader.SortOrder.coordinate.name()); header.setAttribute(SAMFileHeader.SORT_ORDER_TAG, SAMFileHeader.SortOrder.queryname.name()); Assert.assertEquals(header.getSortOrder(), SAMFileHeader.SortOrder.queryname); Assert.assertEquals(header.getAttribute(SAMFileHeader.SORT_ORDER_TAG), SAMFileHeader.SortOrder.queryname.name()); header.setAttribute(SAMFileHeader.SORT_ORDER_TAG, SAMFileHeader.SortOrder.coordinate); Assert.assertEquals(header.getSortOrder(), SAMFileHeader.SortOrder.coordinate); Assert.assertEquals(header.getAttribute(SAMFileHeader.SORT_ORDER_TAG), SAMFileHeader.SortOrder.coordinate.name()); header.setAttribute(SAMFileHeader.SORT_ORDER_TAG, "UNKNOWN"); Assert.assertEquals(header.getSortOrder(), SAMFileHeader.SortOrder.unknown); Assert.assertEquals(header.getAttribute(SAMFileHeader.SORT_ORDER_TAG), SAMFileHeader.SortOrder.unknown.name()); header.setAttribute(SAMFileHeader.SORT_ORDER_TAG, "uNknOWn"); Assert.assertEquals(header.getSortOrder(), SAMFileHeader.SortOrder.unknown); Assert.assertEquals(header.getAttribute(SAMFileHeader.SORT_ORDER_TAG), SAMFileHeader.SortOrder.unknown.name()); header.setAttribute(SAMFileHeader.SORT_ORDER_TAG, "cOoRdinate"); Assert.assertEquals(header.getSortOrder(), SAMFileHeader.SortOrder.unknown); Assert.assertEquals(header.getAttribute(SAMFileHeader.SORT_ORDER_TAG), SAMFileHeader.SortOrder.unknown.name()); }
@Test(dataProvider = "DataForWrongTagTests") public void testSortOrderCodecSetting(String hdr) { String validString = "@HD\tVN:1.0\tSO:unknown\n"; SAMTextHeaderCodec codec = new SAMTextHeaderCodec(); SAMFileHeader header = codec.decode(BufferedLineReader.fromString(validString), null); header.setSortOrder(SAMFileHeader.SortOrder.coordinate); Assert.assertEquals(header.getSortOrder(), SAMFileHeader.SortOrder.coordinate); Assert.assertEquals(header.getAttribute(SAMFileHeader.SORT_ORDER_TAG), SAMFileHeader.SortOrder.coordinate.name()); header.setSortOrder(SAMFileHeader.SortOrder.unsorted); Assert.assertEquals(header.getSortOrder(), SAMFileHeader.SortOrder.unsorted); Assert.assertEquals(header.getAttribute(SAMFileHeader.SORT_ORDER_TAG), SAMFileHeader.SortOrder.unsorted.name()); header.setAttribute(SAMFileHeader.SORT_ORDER_TAG, "badname"); Assert.assertEquals(header.getSortOrder(), SAMFileHeader.SortOrder.unknown); Assert.assertEquals(header.getAttribute(SAMFileHeader.SORT_ORDER_TAG), SAMFileHeader.SortOrder.unknown.name()); header = codec.decode(BufferedLineReader.fromString(hdr), null); Assert.assertTrue(header.getSortOrder().toString().equals("unknown")); }
Assert.assertEquals(fileHeader.getAttribute(charTag), Character.toString(charValue)); final SAMSequenceRecord sequenceRecord = fileHeader.getSequence(sequence); Assert.assertNotNull(sequenceRecord);