@Component public class VcfUtils extends Object
| Constructor and Description |
|---|
VcfUtils() |
| Modifier and Type | Method and Description |
|---|---|
static String |
createId(Entity vcfEntity)
Creates a internal molgenis id from a vcf entity
|
static List<Attribute> |
getAtomicAttributesFromList(Iterable<Attribute> outputAttrs) |
static Map<String,Attribute> |
getAttributesMapFromList(Iterable<Attribute> outputAttrs) |
static String |
getIdFromInfoField(String line) |
static HashMap<String,Trio> |
getPedigree(Scanner inputVcfFileScanner)
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}));
|
protected static String |
toVcfDataType(AttributeType dataType) |
public static String createId(Entity vcfEntity)
vcfEntity - public static List<Attribute> getAtomicAttributesFromList(Iterable<Attribute> outputAttrs)
public static Map<String,Attribute> getAttributesMapFromList(Iterable<Attribute> outputAttrs)
protected static String toVcfDataType(AttributeType dataType)
public static HashMap<String,Trio> getPedigree(Scanner inputVcfFileScanner)
inputVcfFileScanner - FileNotFoundExceptionCopyright © 2017. All Rights Reserved.