htsjdk.samtools.SAMFileWriter Maven / Gradle / Ivy
/*
* The MIT License
*
* Copyright (c) 2009 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 java.io.Closeable;
import htsjdk.samtools.util.ProgressLoggerInterface;
/**
* Interface for SAMText and BAM file writers. Clients need not care which they write to,
* once the object is constructed.
*/
public interface SAMFileWriter extends Closeable {
void addAlignment(SAMRecord alignment);
SAMFileHeader getFileHeader();
/**
* Sets a ProgressLogger on this writer. This is useful when pulling, for instance, from a
* SortingCollection.
*/
void setProgressLogger(final ProgressLoggerInterface progress);
/**
* Must be called to flush or file will likely be defective.
*/
@Override
void close();
}