147 lines
4.8 KiB
Java
147 lines
4.8 KiB
Java
/*
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* Copyright (c) 2012 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package htsjdk.samtools;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.List;
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/**
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* A temporary solution to work around Java access rights issues:
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* override GATKBin and make it public.
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* TODO: Eliminate once we determine the final fate of the BAM index reading code.
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*/
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public class GATKBin implements Comparable<GATKBin> {
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/**
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* The reference sequence associated with this bin.
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*/
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private final int referenceSequence;
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/**
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* The number of this bin within the BAM file.
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*/
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private final int binNumber;
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/**
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* The chunks associated with this bin.
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*/
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private GATKChunk[] chunkList;
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public GATKBin(Bin bin) {
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this(bin.getReferenceSequence(),bin.getBinNumber());
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}
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public GATKBin(final int referenceSequence, final int binNumber) {
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this.referenceSequence = referenceSequence;
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this.binNumber = binNumber;
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}
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public int getReferenceSequence() {
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return referenceSequence;
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}
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public int getBinNumber() {
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return binNumber;
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}
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/**
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* Convert this GATKBin to a normal bin, for processing with the standard BAM query interface.
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* @return
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*/
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public Bin toBin() {
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return new Bin(referenceSequence,binNumber);
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}
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/**
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* See whether two bins are equal. If the ref seq and the bin number
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* are equal, assume equality of the chunk list.
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* @param other The other Bin to which to compare this.
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* @return True if the two bins are equal. False otherwise.
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*/
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@Override
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public boolean equals(Object other) {
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if(other == null) return false;
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if(!(other instanceof GATKBin)) return false;
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GATKBin otherBin = (GATKBin)other;
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return this.referenceSequence == otherBin.referenceSequence && this.binNumber == otherBin.binNumber;
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}
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/**
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* Compute a unique hash code for the given reference sequence and bin number.
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* @return A unique hash code.
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*/
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@Override
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public int hashCode() {
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return ((Integer)referenceSequence).hashCode() ^ ((Integer)binNumber).hashCode();
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}
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/**
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* Compare two bins to see what ordering they should appear in.
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* @param other Other bin to which this bin should be compared.
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* @return -1 if this < other, 0 if this == other, 1 if this > other.
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*/
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public int compareTo(GATKBin other) {
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if(other == null)
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throw new ClassCastException("Cannot compare to a null object");
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// Check the reference sequences first.
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if(this.referenceSequence != other.referenceSequence)
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return referenceSequence - other.referenceSequence;
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// Then check the bin ordering.
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return binNumber - other.binNumber;
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}
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/**
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* Sets the chunks associated with this bin
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*/
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public void setChunkList(GATKChunk[] list){
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chunkList = list;
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}
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/**
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* Gets the list of chunks associated with this bin.
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* @return the chunks in this bin. If no chunks are associated, an empty list will be returned.
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*/
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public GATKChunk[] getChunkList(){
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if(chunkList == null)
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return new GATKChunk[0];
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return chunkList;
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}
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// HACK: Using this classes package permissions to further hack the CRAM created SAMRecord's indexing bin and binary attributes.
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public static Integer getReadIndexingBin(final SAMRecord read) {
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return read.getIndexingBin();
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}
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public static void setReadIndexingBin(final SAMRecord read, final Integer indexingBin) {
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read.setIndexingBin(indexingBin);
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}
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public static SAMBinaryTagAndValue getReadBinaryAttributes(final SAMRecord read) {
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return read.getBinaryAttributes();
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}
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}
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