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A Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework.

There is a newer version: 7.10.0

// Copyright (c) 2017
//
// 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.CachingBAMFileIndex;
import htsjdk.samtools.LinearIndex;
import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.seekablestream.SeekableStream;

/**
 * The htsjdk APIs for accessing the linear BAM index are private...
 */
public class LinearBAMIndex extends CachingBAMFileIndex {

        public LinearBAMIndex(SeekableStream stream, SAMSequenceDictionary dict) {
                super(stream, dict);
        }
        
        public LinearIndex getLinearIndex(int idx) {
                return getQueryResults(idx).getLinearIndex();
        }
}