htsjdk.samtools.SAMSequenceDictionaryCodec Maven / Gradle / Ivy
/*
* The MIT License
*
* Copyright (c) 2016 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools;
import htsjdk.samtools.util.LineReader;
import java.io.Writer;
/**
* "On the fly" codec SAMSequenceDictionaryCodec.
* Encodes each sequence and directly writes it to the Dictionary file.
*
* To use this class you should provide BufferedWriter to it, and so you should close it as you stop using this class.
* You can work with this class as shown below.
*
* Example of using this class:
*
* List dict = ...;
*
* //open BufferedReader and close in try-with-resources
* try(BufferedWriter writer = new BufferedWriter(new FileWriter("path/to/file"))) {
* SAMSequenceDictionaryCodec codec = new SAMSequenceDictionaryCodec(writer);
*
* //we have list of sequences, so encode header line and after that encode each sequence
* codec.encodeHeaderLine(false);
* dict.forEach(codec::encodeSequenceRecord);
*}
*
* or
*
* SAMSequenceDictionary dict = ...;
*
* //open BufferedReader and close in try-with-resources
* try(BufferedWriter writer = new BufferedWriter(new FileWriter("path/to/file"))) {
* SAMSequenceDictionaryCodec codec = new SAMSequenceDictionaryCodec(writer);
*
* //we have complete {@link SAMSequenceDictionary}, so just encode it.
* codec.encode(dict);
*}
*
* @author [email protected], EPAM Systems, Inc.
*/
public class SAMSequenceDictionaryCodec {
private static final SAMFileHeader EMPTY_HEADER = new SAMFileHeader();
private final SAMTextHeaderCodec codec;
public SAMSequenceDictionaryCodec(final Writer writer) {
codec = new SAMTextHeaderCodec();
codec.setmFileHeader(EMPTY_HEADER);
codec.setWriter(writer);
}
/**
* Write {@link SAMSequenceRecord}.
* @param sequenceRecord object to be converted to text.
*/
public void encodeSequenceRecord(final SAMSequenceRecord sequenceRecord) {
codec.encodeSequenceRecord(sequenceRecord);
}
/**
* Write Header line.
* @param keepExistingVersionNumber boolean flag to keep existing version number.
*/
public void encodeHeaderLine(final boolean keepExistingVersionNumber) {
codec.encodeHeaderLine(keepExistingVersionNumber);
}
/**
* Reads text SAM header and converts to a SAMSequenceDictionary object.
* @param reader Where to get header text from.
* @param source Name of the input file, for error messages. May be null.
* @return complete SAMSequenceDictionary object.
*/
public SAMSequenceDictionary decode(final LineReader reader, final String source) {
return codec.decode(reader, source).getSequenceDictionary();
}
/**
* Convert {@link SAMSequenceDictionary} from in-memory representation to text representation.
* @param dictionary object to be converted to text.
*/
public void encode(final SAMSequenceDictionary dictionary) {
codec.encodeHeaderLine(false);
dictionary.getSequences().forEach(this::encodeSequenceRecord);
}
public void setValidationStringency(final ValidationStringency validationStringency) {
codec.setValidationStringency(validationStringency);
}
}