Package htsjdk.samtools
Class SAMTextHeaderCodec
- java.lang.Object
-
- htsjdk.samtools.SAMTextHeaderCodec
-
public class SAMTextHeaderCodec extends Object
Parser for a SAM text header, and a generator of SAM text header.
-
-
Field Summary
Fields Modifier and Type Field Description static String
COMMENT_PREFIX
-
Constructor Summary
Constructors Constructor Description SAMTextHeaderCodec()
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description SAMFileHeader
decode(LineReader reader, String source)
Reads text SAM header and converts to a SAMFileHeader object.void
encode(Writer writer, SAMFileHeader header)
Convert SAMFileHeader from in-memory representation to text representation.void
encode(Writer writer, SAMFileHeader header, boolean keepExistingVersionNumber)
Convert SAMFileHeader from in-memory representation to text representation.protected String
getPGLine(SAMProgramRecord programRecord)
protected String
getRGLine(SAMReadGroupRecord readGroup)
protected String
getSQLine(SAMSequenceRecord sequenceRecord)
void
setValidationStringency(ValidationStringency validationStringency)
-
-
-
Field Detail
-
COMMENT_PREFIX
public static final String COMMENT_PREFIX
-
-
Method Detail
-
decode
public SAMFileHeader decode(LineReader reader, 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(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(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 String getPGLine(SAMProgramRecord programRecord)
-
getRGLine
protected String getRGLine(SAMReadGroupRecord readGroup)
-
getSQLine
protected String getSQLine(SAMSequenceRecord sequenceRecord)
-
setValidationStringency
public void setValidationStringency(ValidationStringency validationStringency)
-
-