gatk-3.8/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java

package org.broadinstitute.sting.utils;

import net.sf.samtools.util.StringUtil;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;

import java.util.Arrays;

/**
 * BaseUtils contains some basic utilities for manipulating nucleotides.
 */
public class BaseUtils {
    public final static byte A = (byte) 'A';
    public final static byte C = (byte) 'C';
    public final static byte G = (byte) 'G';
    public final static byte T = (byte) 'T';

    public final static byte N = (byte) 'N';
    public final static byte D = (byte) 'D';

    //
    // todo -- we need a generalized base abstraction using the Base enum.
    //
    public final static byte[] BASES = {'A', 'C', 'G', 'T'};
    public final static byte[] EXTENDED_BASES = {'A', 'C', 'G', 'T', 'N', 'D'};

    public enum Base {
        A('A', 0),
        C('C', 1),
        G('G', 2),
        T('T', 3);

        byte b;
        int index;

        private Base(char base, int index) {
            this.b = (byte) base;
            this.index = index;
        }

        public byte getBase() { return b; }

        public char getBaseAsChar() { return (char) b; }

        public int getIndex() { return index; }

        public boolean sameBase(byte o) { return b == o; }

        public boolean sameBase(char o) { return b == (byte) o; }

        public boolean sameBase(int i) { return index == i; }
    }

    static private final int[] baseIndexMap = new int[256];
    static {
        Arrays.fill(baseIndexMap, -1);
        baseIndexMap['A'] = 0;
        baseIndexMap['a'] = 0;
        baseIndexMap['*'] = 0;    // the wildcard character counts as an A
        baseIndexMap['C'] = 1;
        baseIndexMap['c'] = 1;
        baseIndexMap['G'] = 2;
        baseIndexMap['g'] = 2;
        baseIndexMap['T'] = 3;
        baseIndexMap['t'] = 3;
    }

    // todo -- fix me (enums?)
    public static final byte DELETION_INDEX = 4;
    public static final byte NO_CALL_INDEX = 5; // (this is 'N')

    public static final int aIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'A');
    public static final int cIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'C');
    public static final int gIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'G');
    public static final int tIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'T');

    /// In genetics, a transition is a mutation changing a purine to another purine nucleotide (A <-> G) or
    // a pyrimidine to another pyrimidine nucleotide (C <-> T).
    // Approximately two out of every three single nucleotide polymorphisms (SNPs) are transitions.
    public enum BaseSubstitutionType {
        TRANSITION,         // A <-> G or C <-> T
        TRANSVERSION
    }

    /**
     * Returns the base substitution type of the 2 state SNP
     *
     * @param base1
     * @param base2
     * @return
     */
    public static BaseSubstitutionType SNPSubstitutionType(byte base1, byte base2) {
        BaseSubstitutionType t = isTransition(base1, base2) ? BaseSubstitutionType.TRANSITION : BaseSubstitutionType.TRANSVERSION;
        //System.out.printf("SNPSubstitutionType( char %c, char %c ) => %s%n", base1, base2, t);
        return t;
    }

    public static boolean isTransition(byte base1, byte base2) {
        int b1 = simpleBaseToBaseIndex(base1);
        int b2 = simpleBaseToBaseIndex(base2);
        return b1 == 0 && b2 == 2 || b1 == 2 && b2 == 0 ||
                b1 == 1 && b2 == 3 || b1 == 3 && b2 == 1;
    }

    public static boolean isTransversion(byte base1, byte base2) {
        return !isTransition(base1, base2);
    }

    /**
     * Private constructor.  No instantiating this class!
     */
    private BaseUtils() {}

    static public boolean basesAreEqual(byte base1, byte base2) {
        return simpleBaseToBaseIndex(base1) == simpleBaseToBaseIndex(base2);
    }

    static public boolean extendedBasesAreEqual(byte base1, byte base2) {
        return extendedBaseToBaseIndex(base1) == extendedBaseToBaseIndex(base2);
    }

    /**
     * @return true iff the bases array contains at least one instance of base
     */
    static public boolean containsBase(final byte[] bases, final byte base) {
        for ( final byte b : bases ) {
            if ( b == base )
                return true;
        }
        return false;
    }

    /**
     * Converts a IUPAC nucleotide code to a pair of bases
     *
     * @param code
     * @return 0, 1, 2, 3, or -1 if the base can't be understood
     */
    @Deprecated
    static public char[] iupacToBases(char code) {
        char[] bases = new char[2];
        switch (code) {
            case '*':               // the wildcard character counts as an A
            case 'A':
            case 'a':
                bases[0] = bases[1] = 'A';
                break;
            case 'C':
            case 'c':
                bases[0] = bases[1] = 'C';
                break;
            case 'G':
            case 'g':
                bases[0] = bases[1] = 'G';
                break;
            case 'T':
            case 't':
                bases[0] = bases[1] = 'T';
                break;
            case 'R':
            case 'r':
                bases[0] = 'A';
                bases[1] = 'G';
                break;
            case 'Y':
            case 'y':
                bases[0] = 'C';
                bases[1] = 'T';
                break;
            case 'S':
            case 's':
                bases[0] = 'G';
                bases[1] = 'C';
                break;
            case 'W':
            case 'w':
                bases[0] = 'A';
                bases[1] = 'T';
                break;
            case 'K':
            case 'k':
                bases[0] = 'G';
                bases[1] = 'T';
                break;
            case 'M':
            case 'm':
                bases[0] = 'A';
                bases[1] = 'C';
                break;
            default:
                bases[0] = bases[1] = 'N';
        }
        return bases;
    }

    /**
     * Converts a simple base to a base index
     *
     * @param base [AaCcGgTt]
     * @return 0, 1, 2, 3, or -1 if the base can't be understood
     */
    static public int simpleBaseToBaseIndex(byte base) {
        return baseIndexMap[base];
    }

    /**
     * Converts a simple base to a base index
     *
     * @param base [AaCcGgTt]
     * @return 0, 1, 2, 3, or -1 if the base can't be understood
     */
    @Deprecated
    static public int simpleBaseToBaseIndex(char base) {
        return baseIndexMap[base];
    }

    static public int extendedBaseToBaseIndex(byte base) {
        switch (base) {
            case 'd':
            case 'D':
                return DELETION_INDEX;
            case 'n':
            case 'N':
                return NO_CALL_INDEX;

            default:
                return simpleBaseToBaseIndex(base);
        }
    }

    @Deprecated
    static public boolean isRegularBase( final char base ) {
        return simpleBaseToBaseIndex(base) != -1;
    }

    static public boolean isRegularBase( final byte base ) {
        return simpleBaseToBaseIndex(base) != -1;
    }

    static public boolean isAllRegularBases( final byte[] bases ) {
        for( final byte base : bases) {
            if( !isRegularBase(base) ) { return false; }
        }
        return true;
    }

    static public boolean isNBase(byte base) {
        return base == 'N' || base == 'n';
    }

    /**
     * Converts a base index to a simple base
     *
     * @param baseIndex 0, 1, 2, 3
     * @return A, C, G, T, or '.' if the index can't be understood
     */
    static public byte baseIndexToSimpleBase(int baseIndex) {
        switch (baseIndex) {
            case 0:
                return 'A';
            case 1:
                return 'C';
            case 2:
                return 'G';
            case 3:
                return 'T';
            default:
                return '.';
        }
    }

    /**
     * Converts a base index to a base index representing its cross-talk partner
     *
     * @param baseIndex 0, 1, 2, 3
     * @return 1, 0, 3, 2, or -1 if the index can't be understood
     */
    static public int crossTalkPartnerIndex(int baseIndex) {
        switch (baseIndex) {
            case 0:
                return 1; // A -> C
            case 1:
                return 0; // C -> A
            case 2:
                return 3; // G -> T
            case 3:
                return 2; // T -> G
            default:
                return -1;
        }
    }

    /**
     * Converts a base to the base representing its cross-talk partner
     *
     * @param base [AaCcGgTt]
     * @return C, A, T, G, or '.' if the base can't be understood
     */
    @Deprecated
    static public char crossTalkPartnerBase(char base) {
        return (char) baseIndexToSimpleBase(crossTalkPartnerIndex(simpleBaseToBaseIndex(base)));
    }

    /**
     * Return the complement of a base index.
     *
     * @param baseIndex the base index (0:A, 1:C, 2:G, 3:T)
     * @return the complementary base index
     */
    static public byte complementIndex(int baseIndex) {
        switch (baseIndex) {
            case 0:
                return 3; // a -> t
            case 1:
                return 2; // c -> g
            case 2:
                return 1; // g -> c
            case 3:
                return 0; // t -> a
            default:
                return -1; // wtf?
        }
    }

    /**
     * Return the complement (A <-> T or C <-> G) of a base, or the specified base if it can't be complemented (i.e. an ambiguous base).
     *
     * @param base the base [AaCcGgTt]
     * @return the complementary base, or the input base if it's not one of the understood ones
     */
    static public byte simpleComplement(byte base) {
        switch (base) {
            case 'A':
            case 'a':
                return 'T';
            case 'C':
            case 'c':
                return 'G';
            case 'G':
            case 'g':
                return 'C';
            case 'T':
            case 't':
                return 'A';
            default:
                return base;
        }
    }

    @Deprecated
    static public char simpleComplement(char base) {
        return (char) simpleComplement((byte) base);
    }

    /**
     * Reverse complement a byte array of bases (that is, chars casted to bytes, *not* base indices in byte form)
     *
     * @param bases the byte array of bases
     * @return the reverse complement of the base byte array
     */
    static public byte[] simpleReverseComplement(byte[] bases) {
        byte[] rcbases = new byte[bases.length];

        for (int i = 0; i < bases.length; i++) {
            rcbases[i] = simpleComplement(bases[bases.length - 1 - i]);
        }

        return rcbases;
    }

    /**
     * Complement a byte array of bases (that is, chars casted to bytes, *not* base indices in byte form)
     *
     * @param bases the byte array of bases
     * @return the complement of the base byte array
     */
    static public byte[] simpleComplement(byte[] bases) {
        byte[] rcbases = new byte[bases.length];

        for (int i = 0; i < bases.length; i++) {
            rcbases[i] = simpleComplement(bases[i]);
        }

        return rcbases;
    }

    /**
     * Reverse complement a char array of bases
     *
     * @param bases the char array of bases
     * @return the reverse complement of the char byte array
     */
    @Deprecated
    static public char[] simpleReverseComplement(char[] bases) {
        char[] rcbases = new char[bases.length];

        for (int i = 0; i < bases.length; i++) {
            rcbases[i] = simpleComplement(bases[bases.length - 1 - i]);
        }

        return rcbases;
    }

    /**
     * Complement a char array of bases
     *
     * @param bases the char array of bases
     * @return the complement of the base char array
     */
    @Deprecated
    static public char[] simpleComplement(char[] bases) {
        char[] rcbases = new char[bases.length];

        for (int i = 0; i < bases.length; i++) {
            rcbases[i] = simpleComplement(bases[i]);
        }

        return rcbases;
    }

    /**
     * Reverse complement a String of bases.  Preserves ambiguous bases.
     *
     * @param bases the String of bases
     * @return the reverse complement of the String
     */
    @Deprecated
    static public String simpleReverseComplement(String bases) {
        return new String(simpleReverseComplement(bases.getBytes()));
    }

    /**
     * Complement a String of bases.  Preserves ambiguous bases.
     *
     * @param bases the String of bases
     * @return the complement of the String
     */
    @Deprecated
    static public String simpleComplement(String bases) {
        return new String(simpleComplement(bases.getBytes()));
    }

    /**
     * Returns the uppercased version of the bases
     *
     * @param bases   the bases
     * @return the upper cased version
     */
    static public void convertToUpperCase(final byte[] bases) {
        StringUtil.toUpperCase(bases);
    }

    /**
     * Returns the index of the most common base in the basecounts array. To be used with
     * pileup.getBaseCounts.
     *
     * @param baseCounts counts of a,c,g,t in order.
     * @return the index of the most common base
     */
    static public int mostFrequentBaseIndex(int[] baseCounts) {
        int mostFrequentBaseIndex = 0;
        for (int baseIndex = 1; baseIndex < 4; baseIndex++) {
            if (baseCounts[baseIndex] > baseCounts[mostFrequentBaseIndex]) {
                mostFrequentBaseIndex = baseIndex;
            }
        }
        return mostFrequentBaseIndex;
    }

    static public int mostFrequentBaseIndexNotRef(int[] baseCounts, int refBaseIndex) {
        int tmp = baseCounts[refBaseIndex];
        baseCounts[refBaseIndex] = -1;
        int result = mostFrequentBaseIndex(baseCounts);
        baseCounts[refBaseIndex] = tmp;
        return result;
    }

    static public int mostFrequentBaseIndexNotRef(int[] baseCounts, byte refSimpleBase) {
        return mostFrequentBaseIndexNotRef(baseCounts, simpleBaseToBaseIndex(refSimpleBase));
    }

    /**
     * Returns the most common base in the basecounts array. To be used with pileup.getBaseCounts.
     *
     * @param baseCounts counts of a,c,g,t in order.
     * @return the most common base
     */
    static public byte mostFrequentSimpleBase(int[] baseCounts) {
        return baseIndexToSimpleBase(mostFrequentBaseIndex(baseCounts));
    }

    /**
     * For the most frequent base in the sequence, return the percentage of the read it constitutes.
     *
     * @param sequence the read sequence
     * @return the percentage of the read that's made up of the most frequent base
     */
    static public double mostFrequentBaseFraction(byte[] sequence) {
        int[] baseCounts = new int[4];

        for (byte base : sequence) {
            int baseIndex = simpleBaseToBaseIndex(base);

            if (baseIndex >= 0) {
                baseCounts[baseIndex]++;
            }
        }

        int mostFrequentBaseIndex = mostFrequentBaseIndex(baseCounts);

        return ((double) baseCounts[mostFrequentBaseIndex]) / ((double) sequence.length);
    }

    // --------------------------------------------------------------------------------
    //
    // random bases
    //
    // --------------------------------------------------------------------------------

    /**
     * Return a random base index (A=0, C=1, G=2, T=3).
     *
     * @return a random base index (A=0, C=1, G=2, T=3)
     */
    static public int getRandomBaseIndex() {
        return getRandomBaseIndex(-1);
    }

    /**
     * Return a random base index, excluding some base index.
     *
     * @param excludeBaseIndex the base index to exclude
     * @return a random base index, excluding the one specified (A=0, C=1, G=2, T=3)
     */
    static public int getRandomBaseIndex(int excludeBaseIndex) {
        int randomBaseIndex = excludeBaseIndex;

        while (randomBaseIndex == excludeBaseIndex) {
            randomBaseIndex = GenomeAnalysisEngine.getRandomGenerator().nextInt(4);
        }

        return randomBaseIndex;
    }

    /**
     * Return a random base (A, C, G, T).
     *
     * @return a random base (A, C, G, T)
     */
    @Deprecated
    static public byte getRandomBase() {
        return getRandomBase('.');
    }

    /**
     * Return a random base, excluding some base.
     *
     * @param excludeBase the base to exclude
     * @return a random base, excluding the one specified (A, C, G, T)
     */
    @Deprecated
    static public byte getRandomBase(char excludeBase) {
        return BaseUtils.baseIndexToSimpleBase(getRandomBaseIndex(BaseUtils.simpleBaseToBaseIndex(excludeBase)));
    }

    /**
     * Computes the smallest period >= minPeriod for the specified string. The period is defined as such p,
     * that for all  i = 0... seq.length-1,  seq[ i % p ] = seq[i] (or equivalently seq[i] = seq[i+p] for i=0...seq.length-1-p).
     * The sequence does <i>not</i> have to contain whole number of periods. For instance, "ACACACAC" has a period
     * of 2 (it has a period of 4 as well), and so does
     * "ACACA"; similarly, smallest periods of "CTCCTC", "CTCCT", and "CTCC" are all equal to 3. The "trivial" period is
     * the length of the string itself, and it will always be returned if no smaller period can be found in the specified period range
     * or if specified minPeriod is greater than the sequence length.
     *
     * @param seq
     * @return
     */
    public static int sequencePeriod(byte[] seq, int minPeriod) {
        int period = (minPeriod > seq.length ? seq.length : minPeriod);
        // we assume that bases [0,period-1] repeat themselves and check this assumption
        // until we find correct period

        for (int pos = period; pos < seq.length; pos++) {

            int offset = pos % period; // we are currenlty 'offset' bases into the putative repeat of period 'period'
            // if our current hypothesis holds, base[pos] must be the same as base[offset]

            if (Character.toUpperCase(seq[pos]) != Character.toUpperCase(seq[offset])) {

                // period we have been trying so far does not work.
                // two possibilities:
                // A) offset = 0, i.e. current position pos must be start of the next repeat, but it is not;
                //      in this case only bases from start up to the current one, inclusive, may form a repeat, if at all;
                //       so period is at least pos+1 (remember, pos is 0-based), then on the next loop re-entrance
                //      pos will be autoincremented and we will be checking next base
                // B) offset != 0, i.e. the current base breaks the repeat, but maybe it starts a new one?
                //     hence we should first check if it matches the first base of the sequence, and to do that
                //     we set period to pos  (thus trying the hypothesis that bases from start up to the current one,
                //     non-inclusive are repeated hereafter), and decrement pos (this will re-test current base against the first base
                // on the next loop re-entrance after pos is autoincremented)
                if (offset == 0)
                    period = pos + 1;
                else
                    period = pos--;

            }
        }
        return period;
    }
}

/* code snippet for testing sequencePeriod():
 * 
 *     	String str = "CCTTG";
    	int p = 0;
    	System.out.print("Periods of " + str +" are:");
    	while ( p < str.length() ) {
    		p = sequencePeriod(str, p+1);
        	System.out.print(" "+p);
    	}
    	System.out.println(); System.exit(1);
*/