Examples with Sample org.molgenis.data.vcf.datastructures.Sample used on opensource projects

Example 1 with Sample

use of org.molgenis.data.vcf.datastructures.Sample in project molgenis by molgenis.

the class VcfUtils method getPedigree.

/**
 * Get pedigree data from VCF Now only support child, father, mother No fancy data structure either Output:
 * result.put(childID, Arrays.asList(new String[]{motherID, fatherID}));
 */
public static HashMap<String, Trio> getPedigree(Scanner inputVcfFileScanner) {
    HashMap<String, Trio> result = new HashMap<>();
    while (inputVcfFileScanner.hasNextLine()) {
        String line = inputVcfFileScanner.nextLine();
        // quit when we don't see header lines anymore
        if (!line.startsWith(VcfRepository.PREFIX)) {
            break;
        }
        // expecting e.g. ##PEDIGREE=<Child=100400,Mother=100402,Father=100401>
        if (line.startsWith("##PEDIGREE")) {
            System.out.println("Pedigree data line: " + line);
            String childID = null;
            String motherID = null;
            String fatherID = null;
            String lineStripped = line.replace("##PEDIGREE=<", "").replace(">", "");
            String[] lineSplit = lineStripped.split(",", -1);
            for (String element : lineSplit) {
                if (element.startsWith("Child")) {
                    childID = element.replace("Child=", "");
                } else if (element.startsWith("Mother")) {
                    motherID = element.replace("Mother=", "");
                } else if (element.startsWith("Father")) {
                    fatherID = element.replace("Father=", "");
                } else {
                    throw new MolgenisDataException("Expected Child, Mother or Father, but found: " + element + " in line " + line);
                }
            }
            if (childID != null && motherID != null && fatherID != null) {
                // good
                result.put(childID, new Trio(new Sample(childID), new Sample(motherID), new Sample(fatherID)));
            } else {
                throw new MolgenisDataException("Missing Child, Mother or Father ID in line " + line);
            }
        }
    }
    return result;
}