/*
* 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;
/**
* A basic interface for querying BAM indices.
*
* @author mhanna
* @version 0.1
*/
public interface BAMIndex extends Closeable {
public static final String BAMIndexSuffix = ".bai";
/**
* Gets the compressed chunks which should be searched for the contents of records contained by the span
* referenceIndex:startPos-endPos, inclusive. See the BAM spec for more information on how a chunk is
* represented.
*
* @param referenceIndex The contig.
* @param startPos Genomic start of query.
* @param endPos Genomic end of query.
* @return A file span listing the chunks in the BAM file.
*/
BAMFileSpan getSpanOverlapping(final int referenceIndex, final int startPos, final int endPos);
/**
* Gets the start of the last linear bin in the index.
* @return The chunk indicating the start of the last bin in the linear index.
*/
long getStartOfLastLinearBin();
/**
* Gets meta data for the given reference including information about number of aligned, unaligned, and noCoordinate records
* @param reference the reference of interest
* @return meta data for the reference
*/
public BAMIndexMetaData getMetaData(int reference);
/**
* Close the index and release any associated resources.
*/
void close();
}