/htsjdk

Add InflaterFactory #771

Merged
merged 1 commit into from Feb 1, 2017
Commits
Jump to file or symbol
Failed to load files and symbols.
+486 −46
Split
View
183 src/main/java/htsjdk/samtools/BAMFileReader.java
@@ -25,13 +25,8 @@
import htsjdk.samtools.seekablestream.SeekableStream;
-import htsjdk.samtools.util.AsyncBlockCompressedInputStream;
-import htsjdk.samtools.util.BinaryCodec;
-import htsjdk.samtools.util.BlockCompressedInputStream;
-import htsjdk.samtools.util.CloseableIterator;
-import htsjdk.samtools.util.CoordMath;
-import htsjdk.samtools.util.RuntimeIOException;
-import htsjdk.samtools.util.StringLineReader;
+import htsjdk.samtools.util.*;
+import htsjdk.samtools.util.zip.InflaterFactory;
import java.io.DataInputStream;
import java.io.File;
@@ -92,40 +87,94 @@
/**
* Prepare to read BAM from a stream (not seekable)
* @param stream source of bytes.
+ * @param indexFile BAM index file
* @param eagerDecode if true, decode all BAM fields as reading rather than lazily.
+ * @param useAsynchronousIO if true, use asynchronous I/O
* @param validationStringency Controls how to handle invalidate reads or header lines.
+ * @param samRecordFactory SAM record factory
+ * @throws IOException
*/
BAMFileReader(final InputStream stream,
final File indexFile,
final boolean eagerDecode,
final boolean useAsynchronousIO,
final ValidationStringency validationStringency,
- final SAMRecordFactory factory)
- throws IOException {
+ final SAMRecordFactory samRecordFactory)
+ throws IOException {
+ this(stream, indexFile, eagerDecode, useAsynchronousIO, validationStringency, samRecordFactory,
+ BlockGunzipper.getDefaultInflaterFactory());
+ }
+
+ /**
+ * Prepare to read BAM from a stream (not seekable)
+ * @param stream source of bytes.
+ * @param indexFile BAM index file
+ * @param eagerDecode if true, decode all BAM fields as reading rather than lazily.
+ * @param useAsynchronousIO if true, use asynchronous I/O
+ * @param validationStringency Controls how to handle invalidate reads or header lines.
+ * @param samRecordFactory SAM record factory
+ * @param inflaterFactory InflaterFactory used by BlockCompressedInputStream
+ * @throws IOException
+ */
+ BAMFileReader(final InputStream stream,
+ final File indexFile,
+ final boolean eagerDecode,
+ final boolean useAsynchronousIO,
+ final ValidationStringency validationStringency,
+ final SAMRecordFactory samRecordFactory,
+ final InflaterFactory inflaterFactory)
+ throws IOException {
mIndexFile = indexFile;
mIsSeekable = false;
- mCompressedInputStream = useAsynchronousIO ? new AsyncBlockCompressedInputStream(stream) : new BlockCompressedInputStream(stream);
+ mCompressedInputStream = useAsynchronousIO ? new AsyncBlockCompressedInputStream(stream, inflaterFactory) : new BlockCompressedInputStream(stream, inflaterFactory);
mStream = new BinaryCodec(new DataInputStream(mCompressedInputStream));
this.eagerDecode = eagerDecode;
this.mValidationStringency = validationStringency;
- this.samRecordFactory = factory;
+ this.samRecordFactory = samRecordFactory;
this.mFileHeader = readHeader(this.mStream, this.mValidationStringency, null);
}
/**
* Prepare to read BAM from a file (seekable)
* @param file source of bytes.
+ * @param indexFile BAM index file
+ * @param eagerDecode if true, decode all BAM fields as reading rather than lazily.
+ * @param useAsynchronousIO if true, use asynchronous I/O
+ * @param validationStringency Controls how to handle invalidate reads or header lines.
+ * @param samRecordFactory SAM record factory
+ * @throws IOException
+ */
+ BAMFileReader(final File file,
+ final File indexFile,
+ final boolean eagerDecode,
+ final boolean useAsynchronousIO,
+ final ValidationStringency validationStringency,
+ final SAMRecordFactory samRecordFactory)
+ throws IOException {
+ this(file, indexFile, eagerDecode, useAsynchronousIO, validationStringency, samRecordFactory, BlockGunzipper.getDefaultInflaterFactory());
+ }
+
+ /**
+ * Prepare to read BAM from a file (seekable)
+ * @param file source of bytes.
+ * @param indexFile BAM index file
* @param eagerDecode if true, decode all BAM fields as reading rather than lazily.
+ * @param useAsynchronousIO if true, use asynchronous I/O
* @param validationStringency Controls how to handle invalidate reads or header lines.
+ * @param samRecordFactory SAM record factory
+ * @param inflaterFactory InflaterFactory used by BlockCompressedInputStream
+ * @throws IOException
*/
BAMFileReader(final File file,
final File indexFile,
final boolean eagerDecode,
final boolean useAsynchronousIO,
final ValidationStringency validationStringency,
- final SAMRecordFactory factory)
+ final SAMRecordFactory samRecordFactory,
+ final InflaterFactory inflaterFactory)
throws IOException {
- this(useAsynchronousIO ? new AsyncBlockCompressedInputStream(file) : new BlockCompressedInputStream(file), indexFile!=null ? indexFile : SamFiles.findIndex(file), eagerDecode, useAsynchronousIO, file.getAbsolutePath(), validationStringency, factory);
+ this(useAsynchronousIO ? new AsyncBlockCompressedInputStream(file, inflaterFactory) : new BlockCompressedInputStream(file, inflaterFactory),
+ indexFile!=null ? indexFile : SamFiles.findIndex(file), eagerDecode, useAsynchronousIO, file.getAbsolutePath(), validationStringency, samRecordFactory);
if (mIndexFile != null && mIndexFile.lastModified() < file.lastModified()) {
System.err.println("WARNING: BAM index file " + mIndexFile.getAbsolutePath() +
" is older than BAM " + file.getAbsolutePath());
@@ -134,60 +183,148 @@
mStream.setInputFileName(file.getAbsolutePath());
}
+ /**
+ * Prepare to read BAM from a stream (seekable)
+ * @param strm source of bytes
+ * @param indexFile BAM index file
+ * @param eagerDecode if true, decode all BAM fields as reading rather than lazily.
+ * @param useAsynchronousIO if true, use asynchronous I/O
+ * @param validationStringency Controls how to handle invalidate reads or header lines.
+ * @param samRecordFactory SAM record factory
+ * @throws IOException
+ */
BAMFileReader(final SeekableStream strm,
final File indexFile,
final boolean eagerDecode,
final boolean useAsynchronousIO,
final ValidationStringency validationStringency,
- final SAMRecordFactory factory)
+ final SAMRecordFactory samRecordFactory)
throws IOException {
- this(useAsynchronousIO ? new AsyncBlockCompressedInputStream(strm) : new BlockCompressedInputStream(strm), indexFile, eagerDecode, useAsynchronousIO, strm.getSource(), validationStringency, factory);
+ this(strm, indexFile, eagerDecode, useAsynchronousIO, validationStringency, samRecordFactory, BlockGunzipper.getDefaultInflaterFactory());
}
+ /**
+ * Prepare to read BAM from a stream (seekable)
+ * @param strm source of bytes
+ * @param indexFile BAM index file
+ * @param eagerDecode if true, decode all BAM fields as reading rather than lazily.
+ * @param useAsynchronousIO if true, use asynchronous I/O
+ * @param validationStringency Controls how to handle invalidate reads or header lines.
+ * @param samRecordFactory SAM record factory
+ * @param inflaterFactory InflaterFactory used by BlockCompressedInputStream
+ * @throws IOException
+ */
+ BAMFileReader(final SeekableStream strm,
+ final File indexFile,
+ final boolean eagerDecode,
+ final boolean useAsynchronousIO,
+ final ValidationStringency validationStringency,
+ final SAMRecordFactory samRecordFactory,
+ final InflaterFactory inflaterFactory)
+ throws IOException {
+ this(useAsynchronousIO ? new AsyncBlockCompressedInputStream(strm, inflaterFactory) : new BlockCompressedInputStream(strm, inflaterFactory),
+ indexFile, eagerDecode, useAsynchronousIO, strm.getSource(), validationStringency, samRecordFactory);
+ }
+
+ /**
+ * Prepare to read BAM from a stream (seekable)
+ * @param strm source of bytes
+ * @param indexStream BAM index stream
+ * @param eagerDecode if true, decode all BAM fields as reading rather than lazily.
+ * @param useAsynchronousIO if true, use asynchronous I/O
+ * @param validationStringency Controls how to handle invalidate reads or header lines.
+ * @param samRecordFactory SAM record factory
+ * @throws IOException
+ */
BAMFileReader(final SeekableStream strm,
final SeekableStream indexStream,
final boolean eagerDecode,
final boolean useAsynchronousIO,
final ValidationStringency validationStringency,
- final SAMRecordFactory factory)
+ final SAMRecordFactory samRecordFactory)
throws IOException {
- this(useAsynchronousIO ? new AsyncBlockCompressedInputStream(strm) : new BlockCompressedInputStream(strm), indexStream, eagerDecode, useAsynchronousIO, strm.getSource(), validationStringency, factory);
+ this(strm, indexStream, eagerDecode, useAsynchronousIO, validationStringency, samRecordFactory, BlockGunzipper.getDefaultInflaterFactory());
}
+ /**
+ * Prepare to read BAM from a stream (seekable)
+ * @param strm source of bytes
+ * @param indexStream BAM index stream
+ * @param eagerDecode if true, decode all BAM fields as reading rather than lazily.
+ * @param useAsynchronousIO if true, use asynchronous I/O
+ * @param validationStringency Controls how to handle invalidate reads or header lines.
+ * @param samRecordFactory SAM record factory
+ * @param inflaterFactory InflaterFactory used by BlockCompressedInputStream
+ * @throws IOException
+ */
+ BAMFileReader(final SeekableStream strm,
+ final SeekableStream indexStream,
+ final boolean eagerDecode,
+ final boolean useAsynchronousIO,
+ final ValidationStringency validationStringency,
+ final SAMRecordFactory samRecordFactory,
+ final InflaterFactory inflaterFactory)
+ throws IOException {
+ this(useAsynchronousIO ? new AsyncBlockCompressedInputStream(strm, inflaterFactory) : new BlockCompressedInputStream(strm, inflaterFactory),
+ indexStream, eagerDecode, useAsynchronousIO, strm.getSource(), validationStringency, samRecordFactory);
+ }
+
+ /**
+ * Prepare to read BAM from a compressed stream (seekable)
+ * @param compressedInputStream source of bytes
+ * @param indexFile BAM index file
+ * @param eagerDecode if true, decode all BAM fields as reading rather than lazily.
+ * @param useAsynchronousIO if true, use asynchronous I/O
+ * @param source string used when reporting errors
+ * @param validationStringency Controls how to handle invalidate reads or header lines.
+ * @param samRecordFactory SAM record factory
+ * @throws IOException
+ */
private BAMFileReader(final BlockCompressedInputStream compressedInputStream,
final File indexFile,
final boolean eagerDecode,
final boolean useAsynchronousIO,
final String source,
final ValidationStringency validationStringency,
- final SAMRecordFactory factory)
+ final SAMRecordFactory samRecordFactory)
throws IOException {
mIndexFile = indexFile;
mIsSeekable = true;
mCompressedInputStream = compressedInputStream;
mStream = new BinaryCodec(new DataInputStream(mCompressedInputStream));
this.eagerDecode = eagerDecode;
this.mValidationStringency = validationStringency;
- this.samRecordFactory = factory;
+ this.samRecordFactory = samRecordFactory;
this.mFileHeader = readHeader(this.mStream, this.mValidationStringency, source);
mFirstRecordPointer = mCompressedInputStream.getFilePointer();
- }
+ }
+ /**
+ * Prepare to read BAM from a compressed stream (seekable)
+ * @param compressedInputStream source of bytes
+ * @param indexStream BAM index stream
+ * @param eagerDecode if true, decode all BAM fields as reading rather than lazily.
+ * @param useAsynchronousIO if true, use asynchronous I/O
+ * @param source string used when reporting errors
+ * @param validationStringency Controls how to handle invalidate reads or header lines.
+ * @param samRecordFactory SAM record factory
+ * @throws IOException
+ */
private BAMFileReader(final BlockCompressedInputStream compressedInputStream,
final SeekableStream indexStream,
final boolean eagerDecode,
final boolean useAsynchronousIO,
final String source,
final ValidationStringency validationStringency,
- final SAMRecordFactory factory)
+ final SAMRecordFactory samRecordFactory)
throws IOException {
mIndexStream = indexStream;
mIsSeekable = true;
mCompressedInputStream = compressedInputStream;
mStream = new BinaryCodec(new DataInputStream(mCompressedInputStream));
this.eagerDecode = eagerDecode;
this.mValidationStringency = validationStringency;
- this.samRecordFactory = factory;
+ this.samRecordFactory = samRecordFactory;
this.mFileHeader = readHeader(this.mStream, this.mValidationStringency, source);
mFirstRecordPointer = mCompressedInputStream.getFilePointer();
}
@@ -234,7 +371,7 @@ protected void enableIndexMemoryMapping(final boolean enabled) {
this.mCompressedInputStream.setCheckCrcs(enabled);
}
- @Override void setSAMRecordFactory(final SAMRecordFactory factory) { this.samRecordFactory = factory; }
+ @Override void setSAMRecordFactory(final SAMRecordFactory samRecordFactory) { this.samRecordFactory = samRecordFactory; }
@Override
public SamReader.Type type() {
Oops, something went wrong.