CramIO (htsjdk 2.8.1 API)

java.lang.Object
- htsjdk.samtools.cram.build.CramIO

```
public class CramIO
extends Object
```
A collection of methods to open and close CRAM files.

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`CRAM_FILE_EXTENSION`
`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()

Constructors
Constructor and Description
`CramIO()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static boolean`	`checkHeaderAndEOF(File file)` Check if the file: 1) contains proper CRAM header.
`static long`	`issueEOF(Version version, OutputStream outputStream)` Write an end-of-file marker to the `OutputStream`.
`static CramHeader`	`readCramHeader(InputStream inputStream)` Read CRAM header from the given `InputStream`.
`static boolean`	`replaceCramHeader(File file, CramHeader newHeader)` Attempt to replace the SAM file header in the CRAM file.
`static long`	`writeCramHeader(CramHeader cramHeader, OutputStream outputStream)` Writes CRAM header into the specified `OutputStream`.
`static long`	`writeHeader(Version cramVersion, OutputStream outStream, SAMFileHeader samFileHeader, String cramID)` Write a CRAM File header and a SAM Header to an output stream.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - CRAM_FILE_EXTENSION
```
public static final String CRAM_FILE_EXTENSION
```
    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.
- Constructor Detail
  - CramIO
```
public CramIO()
```
- Method Detail
  - issueEOF
```
public static long issueEOF(Version version,
                            OutputStream outputStream)
                     throws IOException
```
    Write an end-of-file marker to the OutputStream. The specific EOF marker is chosen based on the CRAM version.
    
    Parameters:
    
    version - the CRAM version to assume
    
    outputStream - the stream to write to
    
    Returns:
    
    the number of bytes written out
    
    Throws:
    
    IOException - as per java IO contract
  - writeHeader
```
public static long writeHeader(Version cramVersion,
                               OutputStream outStream,
                               SAMFileHeader samFileHeader,
                               String cramID)
```
    Write a CRAM File header and a SAM Header to an output stream.
    
    Parameters:
    
    cramVersion -
    
    outStream -
    
    samFileHeader -
    
    cramID -
    
    Returns:
    
    the offset in the stream after writing the headers
  - checkHeaderAndEOF
```
public static boolean checkHeaderAndEOF(File file)
                                 throws IOException
```
    Check if the file: 1) contains proper CRAM header. 2) given the version info from the header check the end of file marker.
    
    Parameters:
    
    file - the CRAM file to check
    
    Returns:
    
    true if the file is a valid CRAM file and is properly terminated with respect to the version.
    
    Throws:
    
    IOException - as per java IO contract
  - writeCramHeader
```
public static long writeCramHeader(CramHeader cramHeader,
                                   OutputStream outputStream)
                            throws IOException
```
    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
    
    Throws:
    
    IOException - as per java IO contract
  - readCramHeader
```
public static CramHeader readCramHeader(InputStream inputStream)
                                 throws IOException
```
    Read CRAM header from the given InputStream.
    
    Parameters:
    
    inputStream - input stream to read from
    
    Returns:
    
    complete CramHeader object
    
    Throws:
    
    IOException - as per java IO contract
  - replaceCramHeader
```
public static boolean replaceCramHeader(File file,
                                        CramHeader newHeader)
                                 throws IOException
```
    Attempt to replace the SAM file header in the CRAM file. This will succeed only if there is sufficient space reserved in the existing CRAM header. The implementation re-writes the first FILE_HEADER block in the first container of the CRAM file using random file access.
    
    Parameters:
    
    file - the CRAM file
    
    newHeader - the new CramHeader container a new SAM file header
    
    Returns:
    
    true if successfully replaced the header, false otherwise
    
    Throws:
    
    IOException - as per java IO contract

Class CramIO

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

CRAM_FILE_EXTENSION

ZERO_B_EOF_MARKER

ZERO_F_EOF_MARKER

Constructor Detail

CramIO

Method Detail

issueEOF

writeHeader

checkHeaderAndEOF

writeCramHeader

readCramHeader

replaceCramHeader