htsjdk.samtools.util.SamRecordWithOrdinal Maven / Gradle / Ivy
/*
* The MIT License
*
* Copyright (c) 2014 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
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools.util;
import htsjdk.samtools.SAMRecord;
/**
* A little class to store the unique index associated with this record. The index is determined as records are read in, so is in fact
* gives the ordinal of the record in the input file. All sub-classes should have a default constructor. Additionally, all implementations
* of this class must implement setResultState, as this class is typically used when wanting to return SAMRecord's in same input order,
* but only when some computation (ex. duplicate marking) has been performed.
*/
public abstract class SamRecordWithOrdinal {
private SAMRecord record;
private long recordOrdinal;
public SamRecordWithOrdinal() {
this.record = null;
this.recordOrdinal = -1;
}
public SamRecordWithOrdinal(final SAMRecord record, final long recordOrdinal) {
this.record = record;
this.recordOrdinal = recordOrdinal;
}
public SAMRecord getRecord() { return this.record; }
public void setRecord(final SAMRecord record) { this.record = record; }
public long getRecordOrdinal() { return this.recordOrdinal; }
public void setRecordOrdinal(final long recordOrdinal) { this.recordOrdinal = recordOrdinal; }
/** Set the result state on this record. */
abstract public void setResultState(final boolean resultState);
}