htsjdk.samtools.LinearIndex 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.util.Arrays;
import java.util.Objects;
/**
* The linear index associated with a given reference in a BAM index.
*
* @author mhanna
* @version 0.1
*/
public class LinearIndex {
public static final int MAX_LINEAR_INDEX_SIZE = GenomicIndexUtil.MAX_LINEAR_INDEX_SIZE;
public static final int BAM_LIDX_SHIFT = 14;
/**
* The reference sequence number for this linear index.
*/
private final int mReferenceSequence;
/**
* Dictates the first stored element of the index.
*/
private final int mIndexStart;
/**
* The linear index entries within this bin.
*/
private final long[] mIndexEntries;
public LinearIndex(final int referenceSequence, final int indexStart, final long[] indexEntries) {
this.mReferenceSequence = referenceSequence;
this.mIndexStart = indexStart;
this.mIndexEntries = indexEntries;
}
public int getReferenceSequence() {
return mReferenceSequence;
}
public int size() {
return mIndexEntries.length;
}
public long get(final int index) {
return mIndexEntries[index-mIndexStart];
}
public static int convertToLinearIndexOffset(final int contigPos) {
final int indexPos = (contigPos <= 0) ? 0 : contigPos-1;
return indexPos >> BAM_LIDX_SHIFT;
}
/**
* Gets the minimum offset of any alignment start appearing in this index, according to the linear index.
* @param startPos Starting position for this query.
* @return The minimum offset, in chunk format, of any read appearing in this position.
*/
public long getMinimumOffset(final int startPos) {
final int start = (startPos <= 0) ? 0 : startPos-1;
final int regionLinearBin = start >> BAM_LIDX_SHIFT;
// System.out.println("# regionLinearBin: " + regionLinearBin);
long minimumOffset = 0;
if (regionLinearBin-mIndexStart < mIndexEntries.length)
minimumOffset = mIndexEntries[regionLinearBin-mIndexStart];
return minimumOffset;
}
/**
* Direct access to the array. Be careful!
* @return The elements of the linear index.
*/
public long[] getIndexEntries() {
return mIndexEntries;
}
public int getIndexStart() {
return mIndexStart;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
LinearIndex that = (LinearIndex) o;
return mReferenceSequence == that.mReferenceSequence &&
mIndexStart == that.mIndexStart &&
Arrays.equals(mIndexEntries, that.mIndexEntries);
}
@Override
public int hashCode() {
int result = Objects.hash(mReferenceSequence, mIndexStart);
result = 31 * result + Arrays.hashCode(mIndexEntries);
return result;
}
}