Package org.broadinstitute.hellbender.tools.walkers.annotator

Class AnnotationUtils

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.annotator.AnnotationUtils

public final class AnnotationUtils
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
static final String	ALLELE_SPECIFIC_RAW_DELIM
static final String	ALLELE_SPECIFIC_REDUCED_DELIM
static final String	ALLELE_SPECIFIC_SPLIT_REGEX
static final String	BRACKET_REGEX
static final String	LIST_DELIMITER

Method Summary

Modifier and Type	Method	Description
static List<String>	decodeAnyASList(String somethingList)	Helper function to convert a comma-separated String (such as a vc.getAttrbute().toString() output) to a List of Strings
static List<String>	decodeAnyASListWithRawDelim(String somethingList)	Helper method to split a "raw" annotation string delimited with "|"
static String	encodeAnyASListWithRawDelim(List<?> somethingList)	Helper function to convert a List of Strings to a @{value ALLELE_SPECIFIC_RAW_DELIM)-separated String, as for raw annotations
static String	encodeStringList(List<String> stringList)	Helper function to convert a List of Strings to a comma-separated String
static String	encodeValueList(List<Double> valueList, String precisionFormat)	Helper function to parse the list into the annotation string
static String	generateMissingDataWarning(htsjdk.variant.variantcontext.VariantContext vc, htsjdk.variant.variantcontext.Genotype g, AlleleLikelihoods<GATKRead,htsjdk.variant.variantcontext.Allele> likelihoods)
static List<String>	getAlleleLengthListOfString(String rawDataString)	Handles all the Java and htsjdk parsing shenanigans
static boolean	isAlleleSpecific(InfoFieldAnnotation annotation)	Helper function to determine if an annotation is allele-specific

Methods inherited from class java.lang.Object

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

Field Details

ALLELE_SPECIFIC_RAW_DELIM

public static final String ALLELE_SPECIFIC_RAW_DELIM

See Also:

• Constant Field Values

ALLELE_SPECIFIC_REDUCED_DELIM

public static final String ALLELE_SPECIFIC_REDUCED_DELIM

See Also:

• Constant Field Values

ALLELE_SPECIFIC_SPLIT_REGEX

public static final String ALLELE_SPECIFIC_SPLIT_REGEX

See Also:

• Constant Field Values

BRACKET_REGEX

public static final String BRACKET_REGEX

See Also:

• Constant Field Values

LIST_DELIMITER

public static final String LIST_DELIMITER

See Also:

• Constant Field Values

Method Details

encodeValueList

public static String encodeValueList(List<Double> valueList,
 String precisionFormat)

Helper function to parse the list into the annotation string

Parameters:

valueList - the ArrayList returned from StrandBiasBySample.annotate()

Returns:

the array used by the per-sample Strand Bias annotation

encodeStringList

public static String encodeStringList(List<String> stringList)

Helper function to convert a List of Strings to a comma-separated String

Parameters:

stringList - the ArrayList with String data

Returns:

a comma-separated String

encodeAnyASListWithRawDelim

public static String encodeAnyASListWithRawDelim(List<?> somethingList)

Helper function to convert a List of Strings to a @{value ALLELE_SPECIFIC_RAW_DELIM)-separated String, as for raw annotations

Parameters:

somethingList - the ArrayList with String data

Returns:

a delimited String

decodeAnyASListWithRawDelim

public static List<String> decodeAnyASListWithRawDelim(String somethingList)

Helper method to split a "raw" annotation string delimited with "|"

Parameters:

somethingList - a String, possibly read from a VCF

Returns:

a List of Strings

decodeAnyASList

public static List<String> decodeAnyASList(String somethingList)

Helper function to convert a comma-separated String (such as a vc.getAttrbute().toString() output) to a List of Strings

Parameters:

somethingList - the allele-specific annotations string; may have brackets

Returns:

a list of allele-specific annotation entries

isAlleleSpecific

public static boolean isAlleleSpecific(InfoFieldAnnotation annotation)

Helper function to determine if an annotation is allele-specific

Parameters:

annotation - the annotation to be tested

Returns:

true if the annotation is expected to have values per-allele

getAlleleLengthListOfString

public static List<String> getAlleleLengthListOfString(String rawDataString)

Handles all the Java and htsjdk parsing shenanigans

Parameters:

rawDataString - should not have surrounding brackets

Returns:

generateMissingDataWarning

public static String generateMissingDataWarning(htsjdk.variant.variantcontext.VariantContext vc,
 htsjdk.variant.variantcontext.Genotype g,
 AlleleLikelihoods<GATKRead,htsjdk.variant.variantcontext.Allele> likelihoods)