VariantEffectPathogenicityScore { public static float getPathogenicityScoreOf(VariantEffect variantEffect) { if (variantEffect == VariantEffect.SEQUENCE_VARIANT) { return NON_PATHOGENIC_SCORE; } if (variantEffect.getImpact().ordinal() > PutativeImpact.MODERATE.ordinal()) { return NON_PATHOGENIC_SCORE; } switch (variantEffect) { case MISSENSE_VARIANT: return DEFAULT_MISSENSE_SCORE; case SYNONYMOUS_VARIANT: return SYNONYMOUS_SCORE; case FRAMESHIFT_ELONGATION: case FRAMESHIFT_TRUNCATION: case FRAMESHIFT_VARIANT: return FRAMESHIFT_SCORE; case MNV: case FEATURE_TRUNCATION: case DISRUPTIVE_INFRAME_DELETION: case DISRUPTIVE_INFRAME_INSERTION: case INFRAME_DELETION: case INFRAME_INSERTION: case INTERNAL_FEATURE_ELONGATION: case COMPLEX_SUBSTITUTION: return NONFRAMESHIFT_INDEL_SCORE; case SPLICE_ACCEPTOR_VARIANT: case SPLICE_DONOR_VARIANT: return SPLICE_DONOR_ACCEPTOR_SCORE; case SPLICE_REGION_VARIANT: return SPLICE_REGION_SCORE; case START_LOST: return STARTLOSS_SCORE; case STOP_LOST: return STOPLOSS_SCORE; case STOP_GAINED: return NONSENSE_SCORE; default: return NON_PATHOGENIC_SCORE; } } private  VariantEffectPathogenicityScore(); static float getPathogenicityScoreOf(VariantEffect variantEffect); static final float DEFAULT_MISSENSE_SCORE; static final float NON_PATHOGENIC_SCORE; static final float FRAMESHIFT_SCORE; static final float NONFRAMESHIFT_INDEL_SCORE; static final float NONSENSE_SCORE; static final float SPLICE_DONOR_ACCEPTOR_SCORE; static final float SPLICE_REGION_SCORE; static final float SYNONYMOUS_SCORE; static final float STOPLOSS_SCORE; static final float STARTLOSS_SCORE; }
@Test public void testGetPathogenicityScoreForDefaultMissense() { VariantEffect variantEffect = VariantEffect.MISSENSE_VARIANT; float result = VariantEffectPathogenicityScore.getPathogenicityScoreOf(variantEffect); assertThat(result, equalTo(VariantEffectPathogenicityScore.DEFAULT_MISSENSE_SCORE)); }
@Test public void testGetPathogenicityScoreForStartLoss() { VariantEffect variantEffect = VariantEffect.START_LOST; float result = VariantEffectPathogenicityScore.getPathogenicityScoreOf(variantEffect); assertThat(result, equalTo(VariantEffectPathogenicityScore.STARTLOSS_SCORE)); }
@Test public void testGetPathogenicityScoreForNonPathogenicVariantType() { VariantEffect variantEffect = VariantEffect.DOWNSTREAM_GENE_VARIANT; float result = VariantEffectPathogenicityScore.getPathogenicityScoreOf(variantEffect); assertThat(result, equalTo(VariantEffectPathogenicityScore.NON_PATHOGENIC_SCORE)); }