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

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.
protected java.lang.String	getPGLine(SAMProgramRecord programRecord)
protected java.lang.String	getRGLine(SAMReadGroupRecord readGroup)
protected java.lang.String	getSQLine(SAMSequenceRecord sequenceRecord)
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.

getPGLine

protected java.lang.String getPGLine(SAMProgramRecord programRecord)

getRGLine

protected java.lang.String getRGLine(SAMReadGroupRecord readGroup)

getSQLine

protected java.lang.String getSQLine(SAMSequenceRecord sequenceRecord)

setValidationStringency

public void setValidationStringency(ValidationStringency validationStringency)