Package htsjdk.samtools
Class SQTagUtil
- java.lang.Object
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- htsjdk.samtools.SQTagUtil
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@Deprecated public class SQTagUtil extends Object
Deprecated.since 11/2018. SQ is a reserved tag that shouldn't be used and this code untested.Utility methods for encoding and decoding the SQ tag value of SAMRecord.
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
SQTagUtil.SQBase
Deprecated.The ordinals of these are stored in the high-order 2 bits of each byte of the SQ tag.
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Field Summary
Fields Modifier and Type Field Description static byte
MAX_QUALITY
Deprecated.
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Constructor Summary
Constructors Constructor Description SQTagUtil()
Deprecated.
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Method Summary
All Methods Static Methods Concrete Methods Deprecated Methods Modifier and Type Method Description static byte
baseAndProbDiffToSqValue(int base, byte probRatio)
Deprecated.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.static byte
baseAndProbDiffToSqValue(SQTagUtil.SQBase base, byte probRatio)
Deprecated.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.static void
reverseComplementSqArray(byte[] sqArray)
Deprecated.Reverses and complements the sqValues in place.static byte
sqScaledProbabilityRatio(double secondBestLikelihood, double thirdBestLikelihood)
Deprecated.Convert a pair of likelihoods into a value suitable for passing to baseAndProbDiffToSqValue.static SQTagUtil.SQBase
sqValueToBase(byte sqValue)
Deprecated.Retrieve the 2nd-best base call from SQ value.static int
sqValueToBaseOrdinal(byte sqValue)
Deprecated.Retrieve the 2nd-best base call from SQ value.static byte
sqValueToProbRatio(byte sqValue)
Deprecated.Retrieve SQ-scaled probability ratio from SQ value.
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Field Detail
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MAX_QUALITY
public static final byte MAX_QUALITY
Deprecated.- See Also:
- Constant Field Values
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Method Detail
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sqScaledProbabilityRatio
public static byte sqScaledProbabilityRatio(double secondBestLikelihood, double thirdBestLikelihood)
Deprecated.Convert a pair of likelihoods into a value suitable for passing to baseAndProbDiffToSqValue.- Parameters:
secondBestLikelihood
- Probability of the 2nd-best base call. 1 > secondBestLikelihood > thirdBestLikelihood.thirdBestLikelihood
- Probability of the 3rd-best base call. thirdBestLikelihood > 0.- Returns:
- ratio of input probabilities for storing in SQ tag.
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baseAndProbDiffToSqValue
public static byte baseAndProbDiffToSqValue(SQTagUtil.SQBase base, byte probRatio)
Deprecated.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.- Parameters:
base
- the 2nd-best base.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.- Returns:
- a byte containing the index and the log probability difference.
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baseAndProbDiffToSqValue
public static byte baseAndProbDiffToSqValue(int base, byte probRatio)
Deprecated.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.- Parameters:
base
- the 2nd-best base (A=0, C=1, G=2, T=3).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.- Returns:
- a byte containing the index and the log probability difference.
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sqValueToProbRatio
public static byte sqValueToProbRatio(byte sqValue)
Deprecated.Retrieve SQ-scaled probability ratio from SQ value.- Parameters:
sqValue
-- Returns:
- the log probability difference between the secondary and tertiary bases (-10log10(p3/p2)).
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sqValueToBase
public static SQTagUtil.SQBase sqValueToBase(byte sqValue)
Deprecated.Retrieve the 2nd-best base call from SQ value.- Parameters:
sqValue
-- Returns:
- 2nd-best base call.
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sqValueToBaseOrdinal
public static int sqValueToBaseOrdinal(byte sqValue)
Deprecated.Retrieve the 2nd-best base call from SQ value.- Parameters:
sqValue
-- Returns:
- Ordinal of 2nd-best base call.
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reverseComplementSqArray
public static void reverseComplementSqArray(byte[] sqArray)
Deprecated.Reverses and complements the sqValues in place.- Parameters:
sqArray
- Array of SQ-values, with 2nd-best base in high-order 2 bits, and probability diff in low-order 6 bits.
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