// insertion G/GA is transferred to nucleotide but not to peptide
"17\t45051613\t.\tG\tGA,C\t1666.64\tRF\tAC=15;AF=3.0e-03,2.0e-03" };
// insertion G/GA is transferred to nucleotide but not to peptide
"17\t45051613\t.\tG\tGA,C\t1666.64\tRF\tAC=15;AF=3.0e-03,2.0e-03" };
Cache.loadProperties("test/jalview/io/testProps.jvprops");
Cache.setProperty("VCF_FIELDS", ".*");
Cache.setProperty("VEP_FIELDS", ".*");
Cache.loadProperties("test/jalview/io/testProps.jvprops");
Cache.setProperty("VCF_FIELDS", ".*");
Cache.setProperty("VEP_FIELDS", ".*");
assertEquals(sf.getFeatureGroup(), "VCF");
assertEquals(sf.getBegin(), 2);
assertEquals(sf.getEnd(), 2);
assertEquals(sf.getFeatureGroup(), "VCF");
assertEquals(sf.getBegin(), 2);
assertEquals(sf.getEnd(), 2);
- assertEquals(sf.getScore(), 4.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 4.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "A,C");
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
sf = geneFeatures.get(1);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "A,C");
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
sf = geneFeatures.get(1);
assertEquals(sf.getBegin(), 2);
assertEquals(sf.getEnd(), 2);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
assertEquals(sf.getBegin(), 2);
assertEquals(sf.getEnd(), 2);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 5.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 5.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "A,T");
sf = geneFeatures.get(2);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "A,T");
sf = geneFeatures.get(2);
assertEquals(sf.getBegin(), 4);
assertEquals(sf.getEnd(), 4);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
assertEquals(sf.getBegin(), 4);
assertEquals(sf.getEnd(), 4);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 2.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,C");
sf = geneFeatures.get(3);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,C");
sf = geneFeatures.get(3);
assertEquals(sf.getBegin(), 4);
assertEquals(sf.getEnd(), 4);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
assertEquals(sf.getBegin(), 4);
assertEquals(sf.getEnd(), 4);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 3.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03,
+ DELTA);
assertEquals(sf.getBegin(), 2);
assertEquals(sf.getEnd(), 2);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
assertEquals(sf.getBegin(), 2);
assertEquals(sf.getEnd(), 2);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 2.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,C");
sf = transcriptFeatures.get(1);
assertEquals(sf.getFeatureGroup(), "VCF");
assertEquals(sf.getBegin(), 2);
assertEquals(sf.getEnd(), 2);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,C");
sf = transcriptFeatures.get(1);
assertEquals(sf.getFeatureGroup(), "VCF");
assertEquals(sf.getBegin(), 2);
assertEquals(sf.getEnd(), 2);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 3.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GA");
/*
* verify SNP variant feature(s) computed and added to protein
* first codon AGC varies to ACC giving S/T
*/
assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GA");
/*
* verify SNP variant feature(s) computed and added to protein
* first codon AGC varies to ACC giving S/T
*/
assertEquals(sf.getBegin(), 24);
assertEquals(sf.getEnd(), 24);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
assertEquals(sf.getBegin(), 24);
assertEquals(sf.getEnd(), 24);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 5.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 5.0e-03,
+ DELTA);
assertEquals(sf.getBegin(), 24);
assertEquals(sf.getEnd(), 24);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
assertEquals(sf.getBegin(), 24);
assertEquals(sf.getEnd(), 24);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 4.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 4.0e-03,
+ DELTA);
assertEquals(sf.getBegin(), 22);
assertEquals(sf.getEnd(), 22);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
assertEquals(sf.getBegin(), 22);
assertEquals(sf.getEnd(), 22);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 2.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03,
+ DELTA);
assertEquals(sf.getBegin(), 21);
assertEquals(sf.getEnd(), 21);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
assertEquals(sf.getBegin(), 21);
assertEquals(sf.getEnd(), 21);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 3.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03,
+ DELTA);
assertEquals(sf.getBegin(), 16);
assertEquals(sf.getEnd(), 16);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
assertEquals(sf.getBegin(), 16);
assertEquals(sf.getEnd(), 16);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 3.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03,
+ DELTA);
assertEquals(sf.getBegin(), 17);
assertEquals(sf.getEnd(), 17);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
assertEquals(sf.getBegin(), 17);
assertEquals(sf.getEnd(), 17);
assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
- assertEquals(sf.getScore(), 2.0e-03, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03,
+ DELTA);
assertEquals(sf.getValue(Gff3Helper.ALLELES), "C,G");
/*
* verify variant feature(s) computed and added to protein
* last codon GCT varies to GGT giving A/G in the last peptide position
*/
assertEquals(sf.getValue(Gff3Helper.ALLELES), "C,G");
/*
* verify variant feature(s) computed and added to protein
* last codon GCT varies to GGT giving A/G in the last peptide position
*/
SequenceFeature sf = geneFeatures.get(0);
assertEquals(sf.getBegin(), 1);
assertEquals(sf.getEnd(), 1);
SequenceFeature sf = geneFeatures.get(0);
assertEquals(sf.getBegin(), 1);
assertEquals(sf.getEnd(), 1);
- assertEquals(sf.getScore(), 0.1f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.1f, DELTA);
assertEquals(sf.getValue("alleles"), "C,A");
// gene features include Consequence for all transcripts
Map map = (Map) sf.getValue("CSQ");
assertEquals(sf.getValue("alleles"), "C,A");
// gene features include Consequence for all transcripts
Map map = (Map) sf.getValue("CSQ");
sf = geneFeatures.get(1);
assertEquals(sf.getBegin(), 5);
assertEquals(sf.getEnd(), 5);
sf = geneFeatures.get(1);
assertEquals(sf.getBegin(), 5);
assertEquals(sf.getEnd(), 5);
- assertEquals(sf.getScore(), 0.2f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.2f, DELTA);
assertEquals(sf.getValue("alleles"), "C,T");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
assertEquals(sf.getValue("alleles"), "C,T");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
sf = geneFeatures.get(2);
assertEquals(sf.getBegin(), 9);
assertEquals(sf.getEnd(), 11); // deletion over 3 positions
sf = geneFeatures.get(2);
assertEquals(sf.getBegin(), 9);
assertEquals(sf.getEnd(), 11); // deletion over 3 positions
- assertEquals(sf.getScore(), 0.3f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.3f, DELTA);
assertEquals(sf.getValue("alleles"), "CGG,C");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
assertEquals(sf.getValue("alleles"), "CGG,C");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
sf = geneFeatures.get(3);
assertEquals(sf.getBegin(), 13);
assertEquals(sf.getEnd(), 13);
sf = geneFeatures.get(3);
assertEquals(sf.getBegin(), 13);
assertEquals(sf.getEnd(), 13);
- assertEquals(sf.getScore(), 0.5f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.5f, DELTA);
assertEquals(sf.getValue("alleles"), "C,T");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
assertEquals(sf.getValue("alleles"), "C,T");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
sf = geneFeatures.get(4);
assertEquals(sf.getBegin(), 13);
assertEquals(sf.getEnd(), 13);
sf = geneFeatures.get(4);
assertEquals(sf.getBegin(), 13);
assertEquals(sf.getEnd(), 13);
- assertEquals(sf.getScore(), 0.4f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.4f, DELTA);
assertEquals(sf.getValue("alleles"), "C,G");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
assertEquals(sf.getValue("alleles"), "C,G");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
sf = geneFeatures.get(5);
assertEquals(sf.getBegin(), 17);
assertEquals(sf.getEnd(), 17);
sf = geneFeatures.get(5);
assertEquals(sf.getBegin(), 17);
assertEquals(sf.getEnd(), 17);
- assertEquals(sf.getScore(), 0.7f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.7f, DELTA);
assertEquals(sf.getValue("alleles"), "A,G");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
assertEquals(sf.getValue("alleles"), "A,G");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
sf = geneFeatures.get(6);
assertEquals(sf.getBegin(), 17);
assertEquals(sf.getEnd(), 17); // insertion
sf = geneFeatures.get(6);
assertEquals(sf.getBegin(), 17);
assertEquals(sf.getEnd(), 17); // insertion
- assertEquals(sf.getScore(), 0.6f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.6f, DELTA);
assertEquals(sf.getValue("alleles"), "A,AC");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
assertEquals(sf.getValue("alleles"), "A,AC");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
sf = transcriptFeatures.get(0);
assertEquals(sf.getBegin(), 3);
assertEquals(sf.getEnd(), 3);
sf = transcriptFeatures.get(0);
assertEquals(sf.getBegin(), 3);
assertEquals(sf.getEnd(), 3);
- assertEquals(sf.getScore(), 0.2f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.2f, DELTA);
assertEquals(sf.getValue("alleles"), "C,T");
// transcript features only have Consequence for that transcripts
map = (Map) sf.getValue("CSQ");
assertEquals(sf.getValue("alleles"), "C,T");
// transcript features only have Consequence for that transcripts
map = (Map) sf.getValue("CSQ");
sf = transcriptFeatures.get(1);
assertEquals(sf.getBegin(), 11);
assertEquals(sf.getEnd(), 11);
sf = transcriptFeatures.get(1);
assertEquals(sf.getBegin(), 11);
assertEquals(sf.getEnd(), 11);
- assertEquals(sf.getScore(), 0.7f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.7f, DELTA);
assertEquals(sf.getValue("alleles"), "A,G");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3");
assertEquals(sf.getValue("alleles"), "A,G");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3");
sf = transcriptFeatures.get(2);
assertEquals(sf.getBegin(), 11);
assertEquals(sf.getEnd(), 11);
sf = transcriptFeatures.get(2);
assertEquals(sf.getBegin(), 11);
assertEquals(sf.getEnd(), 11);
- assertEquals(sf.getScore(), 0.6f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.6f, DELTA);
assertEquals(sf.getValue("alleles"), "A,AC");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3");
assertEquals(sf.getValue("alleles"), "A,AC");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3");
sf = transcriptFeatures.get(0);
assertEquals(sf.getBegin(), 7);
assertEquals(sf.getEnd(), 7);
sf = transcriptFeatures.get(0);
assertEquals(sf.getBegin(), 7);
assertEquals(sf.getEnd(), 7);
- assertEquals(sf.getScore(), 0.5f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.5f, DELTA);
assertEquals(sf.getValue("alleles"), "C,T");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
assertEquals(sf.getValue("alleles"), "C,T");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
sf = transcriptFeatures.get(1);
assertEquals(sf.getBegin(), 7);
assertEquals(sf.getEnd(), 7);
sf = transcriptFeatures.get(1);
assertEquals(sf.getBegin(), 7);
assertEquals(sf.getEnd(), 7);
- assertEquals(sf.getScore(), 0.4f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.4f, DELTA);
assertEquals(sf.getValue("alleles"), "C,G");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
assertEquals(sf.getValue("alleles"), "C,G");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
sf = transcriptFeatures.get(2);
assertEquals(sf.getBegin(), 11);
assertEquals(sf.getEnd(), 11);
sf = transcriptFeatures.get(2);
assertEquals(sf.getBegin(), 11);
assertEquals(sf.getEnd(), 11);
- assertEquals(sf.getScore(), 0.7f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.7f, DELTA);
assertEquals(sf.getValue("alleles"), "A,G");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
assertEquals(sf.getValue("alleles"), "A,G");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
sf = transcriptFeatures.get(3);
assertEquals(sf.getBegin(), 11);
assertEquals(sf.getEnd(), 11);
sf = transcriptFeatures.get(3);
assertEquals(sf.getBegin(), 11);
assertEquals(sf.getEnd(), 11);
- assertEquals(sf.getScore(), 0.6f, DELTA);
+ assertEquals(sf.getScore(), 0f);
+ assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.6f, DELTA);
assertEquals(sf.getValue("alleles"), "A,AC");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
assertEquals(sf.getValue("alleles"), "A,AC");
assertEquals(map.size(), 9);
assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");