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A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
/*
* The MIT License
*
* Copyright (c) 2011 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 picard.illumina.parser;
/**
* Represents one set of cycles in an ReadStructure (e.g. if the ReadStructure is 36TB836T then
* 36T, 8B, and 36T are invidually represented internally as a ReadDescriptor).
*/
public class ReadDescriptor {
public final int length;
public final ReadType type;
public ReadDescriptor(final int length, final ReadType type) {
this.length = length;
this.type = type;
}
@Override
public String toString() {
return this.length + this.type.name();
}
public boolean equals(final Object other) {
if(this == other) return true;
if(other.getClass() != this.getClass()) return false;
final ReadDescriptor that = (ReadDescriptor) other;
return this.length == that.length && this.type == that.type;
}
@Override
public int hashCode() {
return 31 * this.type.ordinal() + 379 * length;
}
}