htsjdk.samtools

Class SAMTextHeaderCodec

java.lang.Object

htsjdk.samtools.SAMTextHeaderCodec

public class SAMTextHeaderCodec
extends java.lang.Object

Parser for a SAM text header, and a generator of SAM text header.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	COMMENT_PREFIX

Constructor Summary

Constructors

Constructor and Description
SAMTextHeaderCodec()

Method Summary

Methods

Modifier and Type	Method and Description
SAMFileHeader	decode(LineReader reader, java.lang.String source) Reads text SAM header and converts to a SAMFileHeader object.
void	encode(java.io.Writer writer, SAMFileHeader header) Convert SAMFileHeader from in-memory representation to text representation.
void	encode(java.io.Writer writer, SAMFileHeader header, boolean keepExistingVersionNumber) Convert SAMFileHeader from in-memory representation to text representation.
void	setValidationStringency(ValidationStringency validationStringency)

Methods inherited from class java.lang.Object

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

Field Detail

COMMENT_PREFIX

public static final java.lang.String COMMENT_PREFIX

Constructor Detail

SAMTextHeaderCodec

public SAMTextHeaderCodec()

Method Detail

decode

public SAMFileHeader decode(LineReader reader,
                   java.lang.String source)

Reads text SAM header and converts to a SAMFileHeader object.

Parameters:

reader - Where to get header text from.

source - Name of the input file, for error messages. May be null.

Returns:

complete header object.

encode

public void encode(java.io.Writer writer,
          SAMFileHeader header)

Convert SAMFileHeader from in-memory representation to text representation. Always writes SAMFileHeader.CURRENT_VERSION as the version in the header.

Parameters:

writer - where to write the header text.

header - object to be converted to text.

encode

public void encode(java.io.Writer writer,
          SAMFileHeader header,
          boolean keepExistingVersionNumber)

Convert SAMFileHeader from in-memory representation to text representation.

Parameters:

writer - where to write the header text.

header - object to be converted to text.

keepExistingVersionNumber - If true, writes whatever version # was in the header. If false, writes SAMFileHeader.CURRENT_VERSION.

setValidationStringency

public void setValidationStringency(ValidationStringency validationStringency)