Examples with VcfRecord org.molgenis.vcf.VcfRecord used on opensource projects

Example 1 with VcfRecord

use of org.molgenis.vcf.VcfRecord in project molgenis by molgenis.

the class VcfToEntityTest method testToEntityMissingValues.

// https://github.com/molgenis/molgenis/issues/5329
@Test
public void testToEntityMissingValues() throws IOException {
    String vcfHeaders = "##fileformat=VCFv4.1\n" + "##INFO=<ID=GoNL_AF,Number=.,Type=Float,Description=\"The allele frequency for variants seen in the population used for the GoNL project\">\n" + "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
    VcfMeta vcfMeta = parseHeaders(vcfHeaders);
    VcfToEntity vcfToEntity = new VcfToEntity("entityTypeName", vcfMeta, vcfAttrs, entityTypeFactory, attrMetaFactory);
    VcfRecord record = new VcfRecord(vcfMeta, new String[] { "1", "54728", ".", "G", "T,C", ".", ".", "GoNL_AF=0.01,." });
    Entity entity = vcfToEntity.toEntity(record);
    assertEquals(entity.getString("GoNL_AF"), "0.01,.");
}

Example 2 with VcfRecord

use of org.molgenis.vcf.VcfRecord in project molgenis by molgenis.

the class VcfToEntityTest method testToEntityAlternativeAlleles.

@Test
public void testToEntityAlternativeAlleles() throws IOException {
    VcfRecord record = new VcfRecord(vcfMetaSmall, new String[] { "10", "12345", "id3", "A", "A,C,G,T,N,*", "7.9123", "pass", "DF;DF2;CHAR=-" });
    Entity entity = vcfToEntitySmall.toEntity(record);
    Entity expected = new DynamicEntity(vcfToEntitySmall.getEntityType());
    expected.set("#CHROM", "10");
    expected.set("ALT", "A,C,G,T,N,*");
    expected.set("POS", 12345);
    expected.set("REF", "A");
    expected.set("FILTER", "pass");
    expected.set("QUAL", "7.9123");
    expected.set("ID", "id3");
    expected.set("INTERNAL_ID", entity.get("INTERNAL_ID"));
    expected.set("DF", true);
    expected.set("DF2", true);
    expected.set("CHAR", "-");
    assertTrue(EntityUtils.equals(entity, expected));
}

Example 3 with VcfRecord

use of org.molgenis.vcf.VcfRecord in project molgenis by molgenis.

the class VcfRepository method iterator.

/**
 * Returns an iterator for this repository.
 * <p>
 * Use with caution! Multiple iterators will all point to the same line in the VCF file, leading to unpredictable
 * behaviour. If you want to get the EntityType of this repository and you can't access getEntityType(),
 * convert the iterator to a PeekingIterator and peek the first Entity.
 */
@Override
public Iterator<Entity> iterator() {
    Iterator<VcfRecord> vcfRecordIterator = Iterators.unmodifiableIterator(vcfReaderFactory.get().iterator());
    VcfToEntity vcfToEntity = vcfToEntitySupplier.get();
    return Iterators.transform(vcfRecordIterator, vcfToEntity::toEntity);
}

Example 4 with VcfRecord

use of org.molgenis.vcf.VcfRecord in project molgenis by molgenis.

the class VcfToEntity method writeInfoFieldsToEntity.

private void writeInfoFieldsToEntity(VcfRecord vcfRecord, Entity entity) {
    // have to contain all flag fields.
    for (String vcfInfoFlagFieldKey : vcfInfoFlagFieldKeys) {
        entity.set(toAttributeName(vcfInfoFlagFieldKey), false);
    }
    for (VcfInfo vcfInfo : vcfRecord.getInformation()) {
        if (// value not available
        vcfInfo.getKey().equals(".")) {
            continue;
        }
        Object val;
        if (vcfInfoFlagFieldKeys.contains(vcfInfo.getKey())) {
            val = true;
        } else {
            Object vcfInfoVal = vcfInfo.getVal();
            if (vcfInfoVal == null) {
                val = null;
            } else if (vcfInfoVal instanceof List<?>) {
                List<?> vcfInfoValTokens = (List<?>) vcfInfoVal;
                // TODO Use list data type once available (see http://www.molgenis.org/ticket/2681)
                val = vcfInfoValTokens.stream().map(vcfInfoValToken -> vcfInfoValToken != null ? vcfInfoValToken.toString() : ".").collect(joining(","));
            } else if (vcfInfoVal instanceof Float) {
                if (Float.isNaN((Float) vcfInfoVal)) {
                    val = null;
                } else {
                    val = new BigDecimal(String.valueOf(vcfInfoVal)).doubleValue();
                }
            } else if (vcfInfoVal instanceof Character) {
                val = vcfInfoVal.toString();
            } else {
                // VCF value type matches type expected for this MOLGENIS attribute type
                val = vcfInfoVal;
            }
        }
        entity.set(toAttributeName(vcfInfo.getKey()), val);
    }
}

Example 5 with VcfRecord

use of org.molgenis.vcf.VcfRecord in project molgenis by molgenis.

the class VcfToEntityTest method testToEntity.

@Test
public void testToEntity() throws IOException {
    VcfRecord record = new VcfRecord(vcfMetaSmall, new String[] { "10", "12345", "id3", "A", "C", "7.9123", "pass", "DF;;CHAR=-" });
    Entity entity = vcfToEntitySmall.toEntity(record);
    Entity expected = new DynamicEntity(vcfToEntitySmall.getEntityType());
    expected.set("#CHROM", "10");
    expected.set("ALT", "C");
    expected.set("POS", 12345);
    expected.set("REF", "A");
    expected.set("FILTER", "pass");
    expected.set("QUAL", "7.9123");
    expected.set("ID", "id3");
    expected.set("INTERNAL_ID", entity.get("INTERNAL_ID"));
    expected.set("DF", true);
    // Flag fields whose flag is not present are set to false
    expected.set("DF2", false);
    expected.set("CHAR", "-");
    assertTrue(EntityUtils.equals(entity, expected));
}