htsjdk.samtools.cram.encoding.core.BetaIntegerCodec Maven / Gradle / Ivy
/**
* ****************************************************************************
* Copyright 2013 EMBL-EBI
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* ****************************************************************************
*/
package htsjdk.samtools.cram.encoding.core;
import htsjdk.samtools.cram.io.BitInputStream;
import htsjdk.samtools.cram.io.BitOutputStream;
/**
* Encodes integers by adding a constant offset value to a range of values in order to reduce
* the necessary number of bits needed to store each value.
*
* As a simple example, consider a data series with values all in the range 10,000 - 10,100.
* Choosing the offset -10,000 means every encoded value will be stored as 0 - 100,
* requiring only ceil(log2(100)) = 7 bits per value.
*/
public class BetaIntegerCodec extends CoreCodec {
private final int offset;
private final int bitsPerValue;
private final long valueLimit; // 1 << bitsPerValue (max 32) so int is too small
/**
* Given integers to encode in the range MIN to MAX:
*
* @param offset the common value to be added to all values before storage.
* Setting this to (-MIN) will ensure all stored values will be in the range (0 .. MAX - MIN)
* @param bitsPerValue the smallest value which will allow the largest stored value (MAX - MIN)
*/
public BetaIntegerCodec(final BitInputStream coreBlockInputStream,
final BitOutputStream coreBlockOutputStream,
final int offset,
final int bitsPerValue) {
super(coreBlockInputStream, coreBlockOutputStream);
this.offset = offset;
this.bitsPerValue = bitsPerValue;
this.valueLimit = 1L << bitsPerValue;
}
@Override
public final Integer read() {
return coreBlockInputStream.readBits(bitsPerValue) - offset;
}
@Override
public Integer read(final int length) {
throw new RuntimeException("Not implemented.");
}
private int getAndCheckOffsetValue(int value) {
final int newValue = value + offset;
if (newValue < 0) {
String negative = String.format("Value %s plus offset %s must be positive",
value, offset);
throw new IllegalArgumentException(negative);
} else if (newValue >= valueLimit) {
String tooBig = String.format("Value %s plus offset %s is greater than or equal to limit %s",
value, offset, valueLimit);
throw new IllegalArgumentException(tooBig);
}
return newValue;
}
@Override
public final void write(final Integer value) {
coreBlockOutputStream.write(getAndCheckOffsetValue(value), bitsPerValue);
}
}