Class SQTagUtil


  • @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.
    • 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.
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static byte MAX_QUALITY
      Deprecated.
       
    • Constructor Summary

      Constructors 
      Constructor Description
      SQTagUtil()
      Deprecated.
       
    • Constructor Detail

      • SQTagUtil

        public SQTagUtil()
        Deprecated.
    • Method Detail

      • 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.
      • 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.
      • 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.
      • 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)).
      • 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.
      • 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.
      • 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.