htsjdk.samtools.cram.build

Class CramIO

java.lang.Object

htsjdk.samtools.cram.build.CramIO

public final class CramIO
extends java.lang.Object

A collection of methods to read and write special values to/from CRAM files.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	CRAM_FILE_EXTENSION Deprecated. since June 2019 Use FileExtensions.CRAM instead.
static int	EOF_ALIGNMENT_SPAN
static int	EOF_ALIGNMENT_START
static int	EOF_BLOCK_SIZE_V2
static int	EOF_BLOCK_SIZE_V3
static byte[]	ZERO_B_EOF_MARKER The 'zero-B' EOF marker as per CRAM specs v2.1.
static byte[]	ZERO_F_EOF_MARKER The zero-F EOF marker as per CRAM specs v3.0.

Constructor Summary

Constructors

Constructor and Description
CramIO()

Method Summary

Modifier and Type	Method and Description
static CramHeader	readCramHeader(java.io.InputStream inputStream) Read CRAM header from the given InputStream.
static byte[]	samHeaderToByteArray(SAMFileHeader samFileHeader)
static long	writeCramEOF(CRAMVersion cramVersion, java.io.OutputStream outputStream) Write an end-of-file marker to the OutputStream.
static long	writeCramHeader(CramHeader cramHeader, java.io.OutputStream outputStream) Writes CRAM header into the specified OutputStream.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

CRAM_FILE_EXTENSION

@Deprecated
public static final java.lang.String CRAM_FILE_EXTENSION

Deprecated. since June 2019 Use FileExtensions.CRAM instead.

See Also:

Constant Field Values

ZERO_B_EOF_MARKER

public static final byte[] ZERO_B_EOF_MARKER

The 'zero-B' EOF marker as per CRAM specs v2.1. This is basically a serialized empty CRAM container with sequence id set to some number to spell out 'EOF' in hex.

ZERO_F_EOF_MARKER

public static final byte[] ZERO_F_EOF_MARKER

The zero-F EOF marker as per CRAM specs v3.0. This is basically a serialized empty CRAM container with sequence id set to some number to spell out 'EOF' in hex.

EOF_ALIGNMENT_START

public static final int EOF_ALIGNMENT_START

See Also:

Constant Field Values

EOF_BLOCK_SIZE_V3

public static final int EOF_BLOCK_SIZE_V3

See Also:

Constant Field Values

EOF_BLOCK_SIZE_V2

public static final int EOF_BLOCK_SIZE_V2

See Also:

Constant Field Values

EOF_ALIGNMENT_SPAN

public static final int EOF_ALIGNMENT_SPAN

See Also:

Constant Field Values

Constructor Detail

CramIO

public CramIO()

Method Detail

writeCramEOF

public static long writeCramEOF(CRAMVersion cramVersion,
                                java.io.OutputStream outputStream)

Write an end-of-file marker to the OutputStream. The specific EOF marker is chosen based on the CRAM version. On read, this is interpreted as a special container sentinel indicating no more containers. The treatment of these EOF markers is asymmetric in that on read, the EOF marker is read in as a special container with sentinel values indicating it is an EOF container (as defined by the spec).

Parameters:

cramVersion - the CRAM version to assume

outputStream - the stream to write to

Returns:

the number of bytes written out

writeCramHeader

public static long writeCramHeader(CramHeader cramHeader,
                                   java.io.OutputStream outputStream)

Writes CRAM header into the specified OutputStream.

Parameters:

cramHeader - the CramHeader object to write

outputStream - the output stream to write to

Returns:

the number of bytes written out

readCramHeader

public static CramHeader readCramHeader(java.io.InputStream inputStream)

Read CRAM header from the given InputStream.

Parameters:

inputStream - input stream to read from

Returns:

complete CramHeader object

samHeaderToByteArray

public static byte[] samHeaderToByteArray(SAMFileHeader samFileHeader)