htsjdk.samtools.util.SolexaQualityConverter Maven / Gradle / Ivy
/*
* The MIT License
*
* Copyright (c) 2009 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 htsjdk.samtools.util;
/**
* Optimized method for converting Solexa ASCII qualities into Phred scores.
* Pre-computes all values in order to eliminate repeated computation.
*/
public class SolexaQualityConverter {
/**
* This value is added to a Solexa quality score to make it printable ASCII
*/
public static final int SOLEXA_ADDEND = 64;
/**
* This value is added to a Phred scord to make it printable ASCII
*/
public static final int PHRED_ADDEND = 33;
/**
* This value is removed from an Illumina 1.8 quality score to make it a Phred score
*/
public final static int ILLUMINA_TO_PHRED_SUBTRAHEND = SOLEXA_ADDEND - PHRED_ADDEND;
private static SolexaQualityConverter singleton = null;
public static synchronized SolexaQualityConverter getSingleton() {
if (singleton == null) {
singleton = new SolexaQualityConverter();
}
return singleton;
}
/**
* Mapping from ASCII value in Gerald export file to phred score
*/
private final byte[] phredScore = new byte[256];
private SolexaQualityConverter() {
for (int i = 0; i < SOLEXA_ADDEND; ++i) {
phredScore[i] = 0;
}
for (int i = SOLEXA_ADDEND; i < phredScore.length; ++i) {
phredScore[i] = convertSolexaQualityCharToPhredBinary(i);
}
}
/** Converts a solexa character quality into a phred numeric quality. */
private byte convertSolexaQualityCharToPhredBinary(final int solexaQuality) {
return (byte) Math.round(10d * Math.log10(1d+Math.pow(10d, (solexaQuality - SOLEXA_ADDEND)/10d)));
}
/**
* Convert a solexa quality ASCII character into a phred score.
*/
public byte solexaCharToPhredBinary(final byte solexaQuality) {
return phredScore[solexaQuality];
}
/**
* @return a byte array that can be indexed by Solexa ASCII quality, with value
* of corresponding Phred score. Elements 0-63 are invalid because Solexa qualities
* should all be >= 64. Do not modify this array!
*/
public byte[] getSolexaToPhredConversionTable() {
return phredScore;
}
/**
* Decodes an array of solexa quality ASCII chars into Phred numeric space.
* Decode in place in order to avoid extra object allocation.
*/
public void convertSolexaQualityCharsToPhredBinary(final byte[] solexaQuals) {
for (int i=0; i