public class SAMSequenceDictionaryCodec extends Object
SAMSequenceDictionary
, so just encode it.
codec.encode(dict);
}Constructor | Description |
---|---|
SAMSequenceDictionaryCodec(BufferedWriter writer) |
Modifier and Type | Method | Description |
---|---|---|
SAMSequenceDictionary |
decode(LineReader reader,
String source) |
Reads text SAM header and converts to a SAMSequenceDictionary object.
|
void |
encode(SAMSequenceDictionary dictionary) |
Convert
SAMSequenceDictionary from in-memory representation to text representation. |
void |
encodeHeaderLine(boolean keepExistingVersionNumber) |
Write Header line.
|
void |
encodeSequenceRecord(SAMSequenceRecord sequenceRecord) |
Write
SAMSequenceRecord . |
void |
setValidationStringency(ValidationStringency validationStringency) |
public SAMSequenceDictionaryCodec(BufferedWriter writer)
public void encodeSequenceRecord(SAMSequenceRecord sequenceRecord)
SAMSequenceRecord
.sequenceRecord
- object to be converted to text.public void encodeHeaderLine(boolean keepExistingVersionNumber)
keepExistingVersionNumber
- boolean flag to keep existing version number.public SAMSequenceDictionary decode(LineReader reader, String source)
reader
- Where to get header text from.source
- Name of the input file, for error messages. May be null.public void encode(SAMSequenceDictionary dictionary)
SAMSequenceDictionary
from in-memory representation to text representation.dictionary
- object to be converted to text.public void setValidationStringency(ValidationStringency validationStringency)