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/*
* 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;
/**
* Utility methods for encoding and decoding the SQ tag value of SAMRecord.
*
* @author [email protected]
* @deprecated since 11/2018. SQ is a reserved tag that shouldn't be used and this code untested.
*/
@Deprecated
public class SQTagUtil {
/**
* The ordinals of these are stored in the high-order 2 bits of each byte of the SQ tag.
* Note that these have the convenient property that the binary complement of each ordinal, masked to
* the two low-order bits, is the complementary base.
*/
public enum SQBase {
SQ_A('A'), SQ_C('C'), SQ_G('G'), SQ_T('T');
private final Character base;
SQBase(final Character base) {
this.base = base;
}
public Character getBase() {
return base;
}
}
/**
* For complementing SQBase ordinals.
*/
private static final int COMPLEMENT_MASK = 3;
private static final int QUALITY_MASK = 0x3f;
public static final byte MAX_QUALITY = QUALITY_MASK;
private static final int BASE_INDEX_SHIFT = 6;
/**
* Convert a pair of likelihoods into a value suitable for passing to baseAndProbDiffToSqValue.
* @param secondBestLikelihood Probability of the 2nd-best base call. 1 > secondBestLikelihood > thirdBestLikelihood.
* @param thirdBestLikelihood Probability of the 3rd-best base call. thirdBestLikelihood > 0.
* @return ratio of input probabilities for storing in SQ tag.
*/
public static byte sqScaledProbabilityRatio(final double secondBestLikelihood, final double thirdBestLikelihood) {
if (secondBestLikelihood >= 1.0 || thirdBestLikelihood <= 0 || thirdBestLikelihood > secondBestLikelihood) {
throw new IllegalArgumentException("Likelihoods out of range. second best: " + secondBestLikelihood +
"; third best: " + thirdBestLikelihood);
}
// Cap value at QUALITY_MASK
return (byte)(Math.min(Math.round(-10.0 * Math.log10(thirdBestLikelihood/secondBestLikelihood)), QUALITY_MASK));
}
/**
* Compress a base and a log probabiliy difference (-10log10(p3/p2)) into
* a single byte so that it can be output in a SAMRecord's SQ field.
*
* @param base the 2nd-best base.
* @param probRatio the log probability difference between the secondary and tertiary bases (-10log10(p3/p2)),
* rounded to an integer and capped so it fits in 6 bits.
* @return a byte containing the index and the log probability difference.
*/
public static byte baseAndProbDiffToSqValue(final SQBase base, final byte probRatio) {
return baseAndProbDiffToSqValue(base.ordinal(), probRatio);
}
/**
* Compress a base and a log probabiliy difference (-10log10(p3/p2)) into
* a single byte so that it can be output in a SAMRecord's SQ field.
*
* @param base the 2nd-best base (A=0, C=1, G=2, T=3).
* @param probRatio the log probability difference between the secondary and tertiary bases (-10log10(p3/p2)),
* rounded to an integer and capped so it fits in 6 bits. If this value is > MAX_QUALITY, it is truncated to that.
* @return a byte containing the index and the log probability difference.
*/
public static byte baseAndProbDiffToSqValue(final int base, final byte probRatio) {
return (byte)((base << BASE_INDEX_SHIFT) | Math.min(probRatio, QUALITY_MASK));
}
/**
* Retrieve SQ-scaled probability ratio from SQ value.
* @param sqValue
* @return the log probability difference between the secondary and tertiary bases (-10log10(p3/p2)).
*/
public static byte sqValueToProbRatio(final byte sqValue) {
return (byte)(sqValue & QUALITY_MASK);
}
/**
* Retrieve the 2nd-best base call from SQ value.
* @param sqValue
* @return 2nd-best base call.
*/
public static SQBase sqValueToBase(final byte sqValue) {
return SQBase.values()[sqValueToBaseOrdinal(sqValue)];
}
/**
* Retrieve the 2nd-best base call from SQ value.
* @param sqValue
* @return Ordinal of 2nd-best base call.
*/
public static int sqValueToBaseOrdinal(final byte sqValue) {
return (sqValue & 0xff) >>> BASE_INDEX_SHIFT;
}
/**
* Reverses and complements the sqValues in place.
* @param sqArray Array of SQ-values, with 2nd-best base in high-order 2 bits, and probability diff
* in low-order 6 bits.
*/
public static void reverseComplementSqArray(final byte[] sqArray) {
final int lastIndex = sqArray.length - 1;
int i, j;
for (i=0, j=lastIndex; i
