org.pharmgkb.parser.vcf

Class VcfUtils

java.lang.Object

org.pharmgkb.parser.vcf.VcfUtils

public class VcfUtils
extends java.lang.Object

Contains static methods for handling properties in INFO and FORMAT fields.

Field Summary

Fields

Modifier and Type	Field and Description
static java.util.regex.Pattern	ALT_BASE_PATTERN
static java.util.regex.Pattern	FILE_FORMAT_PATTERN
static java.util.regex.Pattern	FORMAT_PATTERN
static java.util.regex.Pattern	METADATA_PATTERN
static java.util.regex.Pattern	NUMBER_PATTERN
static java.util.regex.Pattern	REF_BASE_PATTERN
static java.util.regex.Pattern	RSID_PATTERN
static java.util.regex.Pattern	UNQUOTED_EQUAL_SIGN_PATTERN

Constructor Summary

Constructors

Constructor and Description
VcfUtils()

Method Summary

Modifier and Type	Method and Description
static <T> T	convertProperty(java.lang.Class<?> clas, java.lang.String value, boolean isList)
static <T> T	convertProperty(FormatType type, java.lang.String value)
static <T> T	convertProperty(InfoType type, java.lang.String value)
static <T> T	convertProperty(ReservedProperty key, java.lang.String value) Converts a String representation of a property into a more useful type.
static java.util.Map<java.lang.String,java.lang.String>	extractProperties(java.lang.String... props)
static java.util.Map<java.lang.String,java.lang.String>	extractPropertiesFromLine(java.lang.String value)
static java.lang.String	quote(java.lang.String string) Adds double quotation marks around a string.
static org.apache.commons.lang3.tuple.Pair<java.lang.String,java.lang.String>	splitProperty(java.lang.String prop) Splits a property into a key-value pair.
static java.lang.String	unquote(java.lang.String string) Removes double quotation marks around a string if they are present.

Methods inherited from class java.lang.Object

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

Field Detail

ALT_BASE_PATTERN

public static final java.util.regex.Pattern ALT_BASE_PATTERN

REF_BASE_PATTERN

public static final java.util.regex.Pattern REF_BASE_PATTERN

METADATA_PATTERN

public static final java.util.regex.Pattern METADATA_PATTERN

FORMAT_PATTERN

public static final java.util.regex.Pattern FORMAT_PATTERN

RSID_PATTERN

public static final java.util.regex.Pattern RSID_PATTERN

NUMBER_PATTERN

public static final java.util.regex.Pattern NUMBER_PATTERN

FILE_FORMAT_PATTERN

public static final java.util.regex.Pattern FILE_FORMAT_PATTERN

UNQUOTED_EQUAL_SIGN_PATTERN

public static final java.util.regex.Pattern UNQUOTED_EQUAL_SIGN_PATTERN

Constructor Detail

VcfUtils

public VcfUtils()

Method Detail

extractPropertiesFromLine

@Nonnull
public static java.util.Map<java.lang.String,java.lang.String> extractPropertiesFromLine(@Nonnull
                                                                                                   java.lang.String value)

extractProperties

@Nonnull
public static java.util.Map<java.lang.String,java.lang.String> extractProperties(@Nonnull
                                                                                           java.lang.String... props)

splitProperty

@Nonnull
public static org.apache.commons.lang3.tuple.Pair<java.lang.String,java.lang.String> splitProperty(@Nonnull
                                                                                                             java.lang.String prop)

Splits a property into a key-value pair.

Parameters:

prop - In the form "key=value"

quote

@Nonnull
public static java.lang.String quote(@Nonnull
                                               java.lang.String string)

Adds double quotation marks around a string.

unquote

@Nonnull
public static java.lang.String unquote(@Nonnull
                                                 java.lang.String string)

Removes double quotation marks around a string if they are present.

convertProperty

@Nullable
public static <T> T convertProperty(@Nonnull
                                               ReservedProperty key,
                                               @Nullable
                                               java.lang.String value)

Converts a String representation of a property into a more useful type. Specifically, can return:

• String
• Long
• BigDecimal
• The Boolean true (for flags)
• A List of any of the above types

convertProperty

@Nullable
public static <T> T convertProperty(@Nonnull
                                               java.lang.Class<?> clas,
                                               @Nullable
                                               java.lang.String value,
                                               boolean isList)

See Also:

convertProperty(ReservedProperty, String)

convertProperty

@Nullable
public static <T> T convertProperty(@Nonnull
                                               FormatType type,
                                               @Nullable
                                               java.lang.String value)

convertProperty

@Nullable
public static <T> T convertProperty(@Nonnull
                                               InfoType type,
                                               @Nullable
                                               java.lang.String value)