org.molgenis.vcf

Class VcfRecordUtils

java.lang.Object

org.molgenis.vcf.VcfRecordUtils

public class VcfRecordUtils
extends Object

Method Summary

Modifier and Type	Method and Description
static String	getAlt(VcfRecord vcfRecord)
static String	getAlt(VcfRecord vcfRecord, int i)
static int	getAltAlleleIndex(VcfRecord vcfRecord, String alt)
static Double[]	getAltAlleleOrderedDoubleField(VcfRecord vcfRecord, String fieldName)
static int	getAltIndex(VcfRecord vcfRecord, String alt)
static String[]	getAlts(VcfRecord vcfRecord)
static String[]	getAltsAsStringArray(VcfRecord vcfRecord)
static String	getAltString(VcfRecord vcfRecord)
static String	getChrPosRefAlt(VcfRecord vcfRecord)
static String	getId(VcfRecord vcfRecord)
static Optional<VcfInfo>	getInformation(String key, VcfRecord vcfRecord)
static String	getRef(VcfRecord vcfRecord)
static String	getSampleFieldValue(VcfRecord vcfEntity, VcfSample sample, String field)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getInformation

public static Optional<VcfInfo> getInformation(String key,
                                               VcfRecord vcfRecord)

getChrPosRefAlt

public static String getChrPosRefAlt(VcfRecord vcfRecord)

getRef

public static String getRef(VcfRecord vcfRecord)

getAltsAsStringArray

public static String[] getAltsAsStringArray(VcfRecord vcfRecord)

getAltString

public static String getAltString(VcfRecord vcfRecord)

getAlt

public static String getAlt(VcfRecord vcfRecord,
                            int i)

getAlts

public static String[] getAlts(VcfRecord vcfRecord)

getAlt

public static String getAlt(VcfRecord vcfRecord)
                     throws RuntimeException

Throws:

RuntimeException

getAltAlleleIndex

public static int getAltAlleleIndex(VcfRecord vcfRecord,
                                    String alt)

getAltIndex

public static int getAltIndex(VcfRecord vcfRecord,
                              String alt)
                       throws Exception

Throws:

Exception

getId

public static String getId(VcfRecord vcfRecord)

getSampleFieldValue

@Nullable
public static String getSampleFieldValue(VcfRecord vcfEntity,
                                                   VcfSample sample,
                                                   String field)

getAltAlleleOrderedDoubleField

public static Double[] getAltAlleleOrderedDoubleField(VcfRecord vcfRecord,
                                                      String fieldName)