本文整理汇总了Java中htsjdk.samtools.util.IOUtil.maybeBufferedSeekableStream方法的典型用法代码示例。如果您正苦于以下问题：Java IOUtil.maybeBufferedSeekableStream方法的具体用法？Java IOUtil.maybeBufferedSeekableStream怎么用？Java IOUtil.maybeBufferedSeekableStream使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类htsjdk.samtools.util.IOUtil的用法示例。
在下文中一共展示了IOUtil.maybeBufferedSeekableStream方法的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: open
import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
InputStream open(final File file, final boolean seekable, final boolean isGzip, final boolean isBgzf) {
final String filePath = file.getAbsolutePath();
try {
// Open up a buffered stream to read from the file and optionally wrap it in a gzip stream if necessary
if (isBgzf) {
// Only BlockCompressedInputStreams can seek, and only if they are fed a SeekableStream.
return new BlockCompressedInputStream(IOUtil.maybeBufferedSeekableStream(file));
} else if (isGzip) {
if (seekable) {
throw new IllegalArgumentException(
String.format("Cannot create a seekable reader for gzip bcl: %s.", filePath)
);
}
return (IOUtil.maybeBufferInputStream(new GZIPInputStream(new FileInputStream(file), Defaults.BUFFER_SIZE / 2),
Defaults.BUFFER_SIZE / 2));
} else {
if (seekable) {
throw new IllegalArgumentException(
String.format("Cannot create a seekable reader for provided bcl: %s.", filePath)
);
}
return IOUtil.maybeBufferInputStream(new FileInputStream(file));
}
} catch (final FileNotFoundException fnfe) {
throw new PicardException("File not found: (" + filePath + ")", fnfe);
} catch (final IOException ioe) {
throw new PicardException("Error reading file: (" + filePath + ")", ioe);
}
}
示例2: openFile
import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
void openFile() throws IOException {
final BAMIO.ReaderAndIndex r = BAMIO.openBAMAndExposeIndex(storageClient, filePath, ValidationStringency.DEFAULT_STRINGENCY);
reader = r.reader;
indexStream = r.index;
header = reader.getFileHeader();
hasIndex = reader.hasIndex() && reader.indexing().hasBrowseableIndex();
LOG.info("Has index = " + hasIndex);
if (hasIndex) {
index = new BAMFileIndexImpl(
IOUtil.maybeBufferedSeekableStream(indexStream),header.getSequenceDictionary());
} else {
index = null;
}
}