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AlignmentReader.java
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AlignmentReader.java
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/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 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.
*/
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.broad.igv.sam.reader;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.util.CloseableIterator;
import org.broad.igv.sam.Alignment;
import java.io.IOException;
import java.util.List;
import java.util.Map;
import java.util.Set;
/**
* @author jrobinso
*/
public interface AlignmentReader<T extends Alignment> {
void close() throws IOException;
/**
* Return the list of sequence (chromosome) names as defined in the files header or meta-data section.
*/
List<String> getSequenceNames() throws IOException;
default Map<String, Long> getSequenceDictionary() {
return null;
}
/**
* Return the header of the SAM file. May be null
* @return
*/
SAMFileHeader getFileHeader();
/**
* Return the set of all platforms represented in this file.
* May return "null"
*/
Set<String> getPlatforms();
CloseableIterator<T> iterator() throws IOException;
/**
* Query alignments over a given range. Be careful about start/end,
* SAMTools uses 1-based, but IGV uses 0-based.
* This function requires hasIndex() == true.
*
*
* @param sequence
* @param start 0-based start location
* @param end 0-based, exclusive-end coordinate
* @param contained
* @return
* @throws IOException
*/
CloseableIterator<T> query(final String sequence, final int start, final int end, final boolean contained) throws IOException;
default void cancelQuery() {};
boolean hasIndex();
}