Method isLowComplexity2

src/rnabloom/util/SeqUtils.java:370–415

(byte[] bytes)

    }

    public static final boolean isLowComplexity2(byte[] bytes) {
        int length = bytes.length;
        int t1 = Math.min(Byte.MAX_VALUE, Math.round(length * LOW_COMPLEXITY_THRESHOLD_SHORT_SEQ));
        int t2 = Math.min(Byte.MAX_VALUE, Math.round(length * LOW_COMPLEXITY_THRESHOLD_SHORT_SEQ / 2));
        int t3 = Math.min(Byte.MAX_VALUE, Math.round(length * LOW_COMPLEXITY_THRESHOLD_SHORT_SEQ / 3));
        
        byte nf1[]     = new byte[4];
        byte nf2[][]   = new byte[4][4];
        byte nf3[][][] = new byte[4][4][4];
        
        int c3 = nucleotideArrayIndex(bytes[0]);
        int c2 = nucleotideArrayIndex(bytes[1]);
        int c1 = nucleotideArrayIndex(bytes[2]);
        
        ++nf1[c3];
        ++nf1[c2];
        ++nf1[c1];
        
        if (c3 != c2) {
            ++nf2[c3][c2];
        }
        if (c2 != c1) {
            ++nf2[c2][c1];
        }
        
        if (c3 != c2 || c2 != c1 || c3 != c1) {
            ++nf3[c3][c2][c1];
        }
        
        for (int i=3; i<length; ++i) {
            c3 = c2;
            c2 = c1;
            c1 = nucleotideArrayIndex(bytes[i]);
            
            if (++nf1[c1] >= t1)
                return true; // homopolymer runs
            if (c2 != c1 && ++nf2[c2][c1] >= t2)
                return true; // di-nucleotide repeat
            if ((c3 != c2 || c2 != c1 || c3 != c1) && ++nf3[c3][c2][c1] >= t3)
                return true; // tri-nucleotide repeat
        }
        
        // check bias in di/tri-nucleotide content
        return (nf1[0]+nf1[1]>=t1 || nf1[0]+nf1[2]>=t1 || nf1[0]+nf1[3]>=t1 || 
                nf1[1]+nf1[2]>=t1 || nf1[1]+nf1[3]>=t1 || nf1[2]+nf1[3]>=t1);
    }
    
    public static final boolean isRepeat(String seq) {
        final float repeatThreshold = 0.9f;