private static SamReader openBAMReader(SamInputResource resource, ValidationStringency stringency, boolean includeFileSource, long offset) throws IOException { SamReaderFactory samReaderFactory = SamReaderFactory .makeDefault() .validationStringency(stringency) .enable(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES); if (includeFileSource) { samReaderFactory.enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS); } if (offset == 0) { return samReaderFactory.open(resource); } LOG.info("Initializing seeking reader with the offset of " + offset); SeekingBAMFileReader primitiveReader = new SeekingBAMFileReader(resource, false, stringency, DefaultSAMRecordFactory.getInstance(), offset); final SeekingReaderAdapter reader = new SeekingReaderAdapter(primitiveReader, resource); samReaderFactory.reapplyOptions(reader); return reader; } }
private static SamReader openBAMReader(SamInputResource resource, ValidationStringency stringency, boolean includeFileSource, long offset) throws IOException { SamReaderFactory samReaderFactory = SamReaderFactory .makeDefault() .validationStringency(stringency) .enable(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES); if (includeFileSource) { samReaderFactory.enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS); } if (offset == 0) { return samReaderFactory.open(resource); } LOG.info("Initializing seeking reader with the offset of " + offset); SeekingBAMFileReader primitiveReader = new SeekingBAMFileReader(resource, false, stringency, DefaultSAMRecordFactory.getInstance(), offset); final SeekingReaderAdapter reader = new SeekingReaderAdapter(primitiveReader, resource); samReaderFactory.reapplyOptions(reader); return reader; } }
factory.reapplyOptions(samReader);
factory.reapplyOptions(samReader);