htsjdk.samtools.SAMFileSource Maven / Gradle / Ivy
/*
* The MIT License
*
* Copyright (c) 2010 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;
/**
* Represents the origin of a SAM record.
*
* @author mhanna
* @version 0.1
*/
public class SAMFileSource {
/**
* The reader originating this SAM record.
*/
private SamReader mReader;
/**
* The point on disk from which a record originates.
*/
private SAMFileSpan mFilePointer;
/**
* Create a new SAMFileSource with the given reader and file pointer.
* @param reader reader.
* @param filePointer File pointer.
*/
public SAMFileSource(final SamReader reader, final SAMFileSpan filePointer) {
this.mReader = reader;
this.mFilePointer = filePointer;
}
/**
* Retrieves the reader from which this read was initially retrieved.
* @return The reader.
*/
public SamReader getReader() {
return mReader;
}
/**
* A pointer to the region on disk from which the read originated.
* @return A pointer within the file.
*/
public SAMFileSpan getFilePointer() {
return mFilePointer;
}
}