final CachingBAMFileIndex existingIndex = (CachingBAMFileIndex) reader.indexing().getBrowseableIndex(); final int numRefs = existingIndex.getNumberOfReferences(); } else if (SamIndexes.CSI.fileNameSuffix.endsWith(reader.type().indexExtension())) { final CSIIndex existingIndex = (CSIIndex) reader.indexing().getBrowseableIndex(); // new CachingBAMFileIndex(inputBai, null); final int numRefs = existingIndex.getNumberOfReferences();
@BeforeClass public void init() throws IOException { final SamReader reader = SamReaderFactory.makeDefault().enable(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES).open(bamFile); Assert.assertTrue(reader.hasIndex()); Assert.assertTrue(reader.indexing().hasBrowseableIndex()); bamIndex = new GATKBAMIndexFromDataSource(bamFile, reader.getFileHeader(), reader.indexing().getBrowseableIndex()); reader.close(); }
final CachingBAMFileIndex existingIndex = (CachingBAMFileIndex) reader.indexing().getBrowseableIndex(); final int numRefs = existingIndex.getNumberOfReferences();
bamIndices.put(id, new GATKBAMIndexFromDataSource(id.getSamFile(), reader.getFileHeader(), reader.indexing().getBrowseableIndex()));
final CachingBAMFileIndex existingIndex = (CachingBAMFileIndex) reader.indexing().getBrowseableIndex(); // new CachingBAMFileIndex(inputBai, null); final int numRefs = existingIndex.getNumberOfReferences(); final CSIIndex existingIndex = (CSIIndex) reader.indexing().getBrowseableIndex(); // new CachingBAMFileIndex(inputBai, null); final int numRefs = existingIndex.getNumberOfReferences();
final CachingBAMFileIndex existingIndex = (CachingBAMFileIndex) reader.indexing().getBrowseableIndex(); // new CachingBAMFileIndex(inputBai, null); final int numRefs = existingIndex.getNumberOfReferences();
BrowseableBAMIndex index = reader.indexing().getBrowseableIndex();