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.
|
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) |
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.protected java.lang.String getPGLine(SAMProgramRecord programRecord)
protected java.lang.String getRGLine(SAMReadGroupRecord readGroup)
protected java.lang.String getSQLine(SAMSequenceRecord sequenceRecord)
public void setValidationStringency(ValidationStringency validationStringency)