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/*
* The MIT License (MIT)
*
* Copyright (c) 2016 University of California San Diego
* Author: Jim Robinson
*
* 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 org.broad.igv.sam.cram;
import htsjdk.samtools.SAMSequenceRecord;
import htsjdk.samtools.cram.ref.CRAMReferenceSource;
import org.broad.igv.logging.*;
import org.broad.igv.event.GenomeChangeEvent;
import org.broad.igv.event.IGVEventBus;
import org.broad.igv.event.IGVEventObserver;
import org.broad.igv.feature.Chromosome;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.ui.IGV;
import org.broad.igv.util.ObjectCache;
import java.util.HashMap;
/**
* Provide a reference sequence for CRAM decompression. The rule for calculating MD5 is
* to remove any non-base symbols (like \n, sequence name or length and spaces) and upper case the rest.
*/
public class IGVReferenceSource implements CRAMReferenceSource {
private static Logger log = LogManager.getLogger(IGVReferenceSource.class);
@Override
public byte[] getReferenceBases(SAMSequenceRecord record, boolean tryNameVariants) {
return getReferenceBasesByRegion(record, 0, record.getSequenceLength());
}
public byte[] getReferenceBasesByRegion(final SAMSequenceRecord sequenceRecord, final int zeroBasedStart, final int requestedRegionLength) {
final String name = sequenceRecord.getSequenceName();
final Genome currentGenome = GenomeManager.getInstance().getCurrentGenome();
String chrName = currentGenome.getCanonicalChrName(name);
byte[] bases = currentGenome.getSequence(chrName, zeroBasedStart, zeroBasedStart + requestedRegionLength, true);
// CRAM spec requires upper case
for (int i = 0; i < bases.length; i++) {
if (bases[i] >= 97) bases[i] -= 32;
}
return bases;
}
}
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