private void transformQualityScoresArray(int oldEncoding, int newEncoding) {
        // If the score types of the encodings are different
        if (FastQ.SCALE_SCORE[oldEncoding] != FastQ.SCALE_SCORE[newEncoding]) {
            // Score Map selection
            Map<Integer, Integer> scoreMap;
            if (FastQ.SCALE_SCORE[oldEncoding] == FastQ.PHRED_SCORE_TYPE) {
                scoreMap = FastQ.phredToSolexaMap;
            } else {
                scoreMap = FastQ.solexaToPhredMap;
            }
            // Transform each quality score in the quality scores array
            for (int i = 0; i < this.qualityScoresArray.length; i++) {
                if (qualityScoresArray[i] < 10) {
                    qualityScoresArray[i] = scoreMap.get(qualityScoresArray[i]);
                }
            }
        }
    }
private void transformQualityScoresArray ( int oldEncoding , int newEncoding ) { if ( FastQ . SCALE_SCORE [ oldEncoding ] != FastQ . SCALE_SCORE [ newEncoding ] ) { Map < Integer , Integer > scoreMap ; if ( FastQ . SCALE_SCORE [ oldEncoding ] == FastQ . PHRED_SCORE_TYPE ) { scoreMap = FastQ . phredToSolexaMap ; } else { scoreMap = FastQ . solexaToPhredMap ; } for ( int i = 0 ; i < this . qualityScoresArray . length ; i ++ ) { if ( qualityScoresArray [ i ] < 10 ) { qualityScoresArray [ i ] = scoreMap . get ( qualityScoresArray [ i ] ) ; } } } }
Transform the quality scores array if the score types of the encodings are different

@param oldEncoding - old quality encoding type
@param newEncoding - new quality encoding type