public class SAMTextHeaderCodec
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static java.lang.String |
COMMENT_PREFIX |
Constructor and Description |
---|
SAMTextHeaderCodec() |
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) |
public SAMFileHeader decode(LineReader reader, java.lang.String source)
reader
- Where to get header text from.source
- Name of the input file, for error messages. May be null.public void encode(java.io.Writer writer, SAMFileHeader header)
writer
- where to write the header text.header
- object to be converted to text.public void encode(java.io.Writer writer, SAMFileHeader header, boolean keepExistingVersionNumber)
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.public void setValidationStringency(ValidationStringency validationStringency)