public class SAMSequenceDictionaryCodec
extends java.lang.Object
SAMSequenceDictionary
, so just encode it.
codec.encode(dict);
}Constructor and Description |
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SAMSequenceDictionaryCodec(java.io.BufferedWriter writer) |
Modifier and Type | Method and Description |
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SAMSequenceDictionary |
decode(LineReader reader,
java.lang.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(java.io.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, 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(SAMSequenceDictionary dictionary)
SAMSequenceDictionary
from in-memory representation to text representation.dictionary
- object to be converted to text.public void setValidationStringency(ValidationStringency validationStringency)