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

Example 1 with VcfInfo

use of org.molgenis.vcf.VcfInfo 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);
    }
}