Package org.pharmgkb.parser.vcf

Class VcfUtils

java.lang.Object

org.pharmgkb.parser.vcf.VcfUtils

public class VcfUtils
extends Object

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

Field Summary

Fields

Modifier and Type	Field	Description
static final Pattern	ALT_BASE_PATTERN
static final Pattern	FILE_FORMAT_PATTERN
static final Pattern	FORMAT_PATTERN
static final Pattern	METADATA_PATTERN
static final Pattern	NUMBER_PATTERN
static final Pattern	REF_BASE_PATTERN
static final Pattern	RSID_PATTERN
static final Pattern	UNQUOTED_EQUAL_SIGN_PATTERN

Constructor Summary

Constructors

Constructor	Description
VcfUtils()

Method Summary

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

ALT_BASE_PATTERN

public static final Pattern ALT_BASE_PATTERN

REF_BASE_PATTERN

public static final Pattern REF_BASE_PATTERN

METADATA_PATTERN

public static final Pattern METADATA_PATTERN

FORMAT_PATTERN

public static final Pattern FORMAT_PATTERN

RSID_PATTERN

public static final Pattern RSID_PATTERN

NUMBER_PATTERN

public static final Pattern NUMBER_PATTERN

FILE_FORMAT_PATTERN

public static final Pattern FILE_FORMAT_PATTERN

UNQUOTED_EQUAL_SIGN_PATTERN

public static final Pattern UNQUOTED_EQUAL_SIGN_PATTERN

Constructor Details

VcfUtils

public VcfUtils()

Method Details

extractPropertiesFromLine

@Nonnull
public static Map<String,String> extractPropertiesFromLine(@Nonnull
 String value)

extractProperties

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

splitProperty

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

Splits a property into a key-value pair.

Parameters:

prop - In the form "key=value"

quote

@Nonnull
public static String quote(@Nonnull
 String string)

Adds double quotation marks around a string.

unquote

@Nonnull
public static String unquote(@Nonnull
 String string)

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

convertProperty

@Nullable
public static <T> T convertProperty(@Nonnull
 ReservedProperty key,
 @Nullable
 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
 Class<?> clas,
 @Nullable
 String value,
 boolean isList)

See Also:

• convertProperty(ReservedProperty, String)

convertProperty

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

convertProperty

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