org.broadinstitute.hellbender.utils

Class Utils

java.lang.Object

org.broadinstitute.hellbender.utils.Utils

public final class Utils
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static java.util.Comparator<? super java.lang.String>	COMPARE_STRINGS_NULLS_FIRST Comparator for strings that sorts null first;
static float	JAVA_DEFAULT_HASH_LOAD_FACTOR

Method Summary

Modifier and Type	Method and Description
static <T> java.util.List<T>	append(java.util.List<T> left, T... elts) Create a new list that contains the elements of left along with elements elts
static java.util.List<java.lang.Double>	asList(double... values) Returns a List<Double> representation of an primitive double array.
static java.util.List<java.lang.Integer>	asList(int... values) Returns a List<Integer> representation of an primitive int array.
static java.lang.String	calcMD5(byte[] bytes) Calculate the md5 for bytes, and return the result as a 32 character string
static java.lang.String	calcMD5(java.lang.String s)
static java.lang.String	calculateFileMD5(java.io.File file) Calculates the MD5 for the specified file and returns it as a String
static java.lang.String	calculatePathMD5(java.nio.file.Path path) Calculates the MD5 for the specified file and returns it as a String
static <E> java.util.Set<E>	checkForDuplicatesAndReturnSet(java.util.Collection<E> c, java.lang.String message) Checks that the collection does not contain a duplicate value (throws an IllegalArgumentException if it does).
static byte[]	concat(byte[]... allBytes) Concatenates byte arrays
static byte[]	concat(byte[] a, byte[] b) Concats two byte arrays.
static <T> T[]	concat(T[] a, T[] b, java.util.function.IntFunction<T[]> constructor)
static <T> java.util.Iterator<T>	concatIterators(java.util.Iterator<? extends java.lang.Iterable<T>> iterator) Concatenates a series of Iterators (all of the same type) into a single Iterator.
static <T> java.util.List<T>	cons(T elt, java.util.List<T> l)
static void	containsNoNull(java.util.Collection<?> collection, java.lang.String message) Checks that the collection does not contain a null value (throws an IllegalArgumentException if it does).
static int	countBooleanOccurrences(boolean element, boolean[] array) Returns the number of occurrences of a boolean element in a boolean array.
static byte[]	dupBytes(byte b, int nCopies) Create a new byte array that's n copies of b
static java.lang.String	dupChar(char c, int nCopies) Create a new string that's n copies of c
static java.lang.String	dupString(java.lang.String s, int nCopies) Create a new string thats a n duplicate copies of s
static boolean	equalRange(byte[] left, int leftOffset, byte[] right, int rightOffset, int length) Compares sections from to byte arrays to verify whether they contain the same values.
static java.lang.String[]	escapeExpressions(java.lang.String args) Splits expressions in command args by spaces and returns the array of expressions.
static java.util.Set<java.lang.String>	filterCollectionByExpressions(java.util.Collection<java.lang.String> sourceValues, java.util.Collection<java.lang.String> filterExpressions, boolean exactMatch) Given a collection of strings and a collection of regular expressions, generates the set of strings that match any expression
static void	forceJVMLocaleToUSEnglish() Set the Locale to US English so that numbers will always be formatted in the US style.
static java.lang.String	formattedPercent(long x, long total) Convenience function that formats a percentage as a %.2f string
static java.lang.String	formattedRatio(long num, long denom) Convenience function that formats a ratio as a %.2f string
static java.lang.String	getDateTimeForDisplay(java.time.ZonedDateTime dateTime) Return the given dateTime formatted as string for display.
static <T> java.util.Set<T>	getDuplicatedItems(java.util.Collection<T> objects) Gets duplicated items in the collection.
static <T extends java.lang.Comparable<?>> T	getMedianValue(java.util.List<T> values) Streams and sorts a collection of objects and returns the integer median entry of the sorted list
static org.apache.commons.math3.random.RandomDataGenerator	getRandomDataGenerator()
static java.util.Random	getRandomGenerator()
static <T,U> java.util.Map<U,java.util.Set<T>>	getReverseValueToListMap(java.util.Map<T,java.util.List<U>> somethingToListMap) Take a map of a value to a list and reverse it.
static <T> java.util.function.Function<T,T>	identityFunction() Returns a function that always returns its input argument.
static boolean	isNonEmpty(java.util.Collection<?> collection) Checks that a Collection is not null and that it is not empty.
static java.lang.String	join(java.lang.CharSequence separator, java.lang.Object... objects) Returns a string of the values in an Object array joined by a separator.
static <T> java.lang.String	join(java.lang.String separator, java.util.Collection<T> objects) Returns a string of the form elt1.toString() [sep elt2.toString() ...
static java.lang.String	join(java.lang.String separator, double[] doubles) Returns a string of the values in joined by separator, such as A,B,C
static java.lang.String	join(java.lang.String separator, int[] ints) Returns a string of the values in ints joined by separator, such as A,B,C
static int	lastIndexOf(byte[] reference, byte[] query) Find the last occurrence of the query sequence in the reference sequence Returns the index of the last occurrence or -1 if the query sequence is not found
static java.util.List<java.lang.Integer>	listFromPrimitives(int[] ar) Simple wrapper for sticking elements of a int[] array into a List
static <T> java.util.List<java.util.List<T>>	makePermutations(java.util.List<T> objects, int n, boolean withReplacement) Make all combinations of N size of objects if objects = [A, B, C] if N = 1 => [[A], [B], [C]] if N = 2 => [[A, A], [B, A], [C, A], [A, B], [B, B], [C, B], [A, C], [B, C], [C, C]]
static java.lang.String	nonEmpty(java.lang.String string) Checks that a String is not null and that it is not empty.
static java.lang.String	nonEmpty(java.lang.String string, java.lang.String message) Checks that a String is not null and that it is not empty.
static <I,T extends java.util.Collection<I>> T	nonEmpty(T collection) Checks that a Collection is not null and that it is not empty.
static <I,T extends java.util.Collection<I>> T	nonEmpty(T collection, java.lang.String message) Checks that a Collection is not null and that it is not empty.
static <T> T	nonNull(T object) Checks that an Object object is not null and returns the same object or throws an IllegalArgumentException
static <T> T	nonNull(T object, java.lang.String message) Checks that an Object is not null and returns the same object or throws an IllegalArgumentException
static <T> T	nonNull(T object, java.util.function.Supplier<java.lang.String> message) Checks that an Object is not null and returns the same object or throws an IllegalArgumentException
static int	optimumHashSize(int maxElements) Calculates the optimum initial size for a hash table given the maximum number of elements it will need to hold.
static byte[]	repeatBytes(byte b, int n) makes an array filled with n copies of the given byte.
static byte[]	repeatChars(char c, int n) makes an array filled with n copies of the given char.
static void	resetRandomGenerator()
static <T> T	runInParallel(int threads, java.util.function.Supplier<T> supplier) Runs a task in parallel returning it returned result.
static <T> T	skimArray(T original, boolean[] remove) Skims out positions of an array returning a shorter one with the remaning positions in the same order.
static <T> T	skimArray(T source, int sourceOffset, T dest, int destOffset, boolean[] remove, int removeOffset) Skims out positions of an array returning a shorter one with the remaining positions in the same order.
static <T> T	skimArray(T source, int sourceOffset, T dest, int destOffset, boolean[] remove, int removeOffset, int length) Skims out positions of an array returning a shorter one with the remaning positions in the same order.
static java.util.List<java.lang.String>	split(java.lang.String str, char delimiter) Splits a String using indexOf instead of regex to speed things up.
static java.util.List<java.lang.String>	split(java.lang.String str, java.lang.String delimiter) Splits a String using indexOf instead of regex to speed things up.
static <T> java.util.stream.Stream<T>	stream(java.util.Enumeration<T> enumeration)
static <T> java.util.stream.Stream<T>	stream(java.lang.Iterable<T> iterable)
static <T> java.util.stream.Stream<T>	stream(java.util.Iterator<T> iterator)
static <F,T> java.util.Iterator<T>	transformParallel(java.util.Iterator<F> fromIterator, java.util.function.Function<F,T> function, int numThreads) Like Guava's Iterators.transform(Iterator, com.google.common.base.Function), but runs a fixed number (numThreads) of transformations in parallel, while maintaining ordering of the output iterator.
static void	validate(boolean condition, java.lang.String msg) Check a condition that should always be true and throw an IllegalStateException if false.
static void	validate(boolean condition, java.util.function.Supplier<java.lang.String> msg) Check a condition that should always be true and throw an IllegalStateException if false.
static void	validateArg(boolean condition, java.lang.String msg)
static void	validateArg(boolean condition, java.util.function.Supplier<java.lang.String> msg)
static int	validIndex(int index, int length) Checks whether an index is within bounds considering a collection or array of a particular size whose first position index is 0
static int	validIndex(int index, int length, java.lang.String errorMessage) Checks whether an index is within bounds considering a collection or array of a particular size whose first position index is 0
static void	warnOnNonIlluminaReadGroups(htsjdk.samtools.SAMFileHeader readsHeader, org.apache.logging.log4j.Logger logger) Checks if the read header contains any reads groups from non-Illumina and issue a warning of that's the case.
static void	warnUser(org.apache.logging.log4j.Logger logger, java.lang.String msg)
static void	warnUser(java.lang.String msg)
static java.util.List<java.lang.String>	warnUserLines(java.lang.String msg)
static boolean	xor(boolean x, boolean y) Boolean xor operation.

Methods inherited from class java.lang.Object

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

Field Detail

COMPARE_STRINGS_NULLS_FIRST

public static final java.util.Comparator<? super java.lang.String> COMPARE_STRINGS_NULLS_FIRST

Comparator for strings that sorts null first;

JAVA_DEFAULT_HASH_LOAD_FACTOR

public static final float JAVA_DEFAULT_HASH_LOAD_FACTOR

See Also:

Constant Field Values

Method Detail

getRandomGenerator

public static java.util.Random getRandomGenerator()

getRandomDataGenerator

public static org.apache.commons.math3.random.RandomDataGenerator getRandomDataGenerator()

resetRandomGenerator

public static void resetRandomGenerator()

cons

public static <T> java.util.List<T> cons(T elt,
                                         java.util.List<T> l)

warnUser

public static void warnUser(java.lang.String msg)

warnUser

public static void warnUser(org.apache.logging.log4j.Logger logger,
                            java.lang.String msg)

warnUserLines

public static java.util.List<java.lang.String> warnUserLines(java.lang.String msg)

join

public static java.lang.String join(java.lang.CharSequence separator,
                                    java.lang.Object... objects)

Returns a string of the values in an Object array joined by a separator.

Parameters:

separator - separator character

objects - the array with values

Returns:

a string with the values separated by the separator

Throws:

java.lang.IllegalArgumentException - if separator or objects is null.

join

public static java.lang.String join(java.lang.String separator,
                                    int[] ints)

Returns a string of the values in ints joined by separator, such as A,B,C

Parameters:

separator - separator character

ints - the array with values

Returns:

a string with the values separated by the separator

join

public static java.lang.String join(java.lang.String separator,
                                    double[] doubles)

Returns a string of the values in joined by separator, such as A,B,C

Parameters:

separator - separator character

doubles - the array with values

Returns:

a string with the values separated by the separator

join

public static <T> java.lang.String join(java.lang.String separator,
                                        java.util.Collection<T> objects)

Returns a string of the form elt1.toString() [sep elt2.toString() ... sep elt.toString()] for a collection of elti objects (note there's no actual space between sep and the elti elements). Returns "" if collection is empty. If collection contains just elt, then returns elt.toString()

Type Parameters:

T - the type of the objects

Parameters:

separator - the string to use to separate objects

objects - a collection of objects. the element order is defined by the iterator over objects

Returns:

a non-null string

concat

public static byte[] concat(byte[]... allBytes)

Concatenates byte arrays

Returns:

a concat of all bytes in allBytes in order

concat

public static <T> T[] concat(T[] a,
                             T[] b,
                             java.util.function.IntFunction<T[]> constructor)

concat

public static byte[] concat(byte[] a,
                            byte[] b)

Concats two byte arrays.

A bit more efficient than calling the more general #concat(byte[]...).

Parameters:

a - left array to concat.

b - right array to concat.

Returns:

never null;

asList

public static java.util.List<java.lang.Integer> asList(int... values)

Returns a List<Integer> representation of an primitive int array.

Parameters:

values - the primitive int array to represent.

Returns:

never code null. The returned list will be unmodifiable yet it will reflect changes in values in the original array yet you cannot change the values

asList

public static java.util.List<java.lang.Double> asList(double... values)

Returns a List<Double> representation of an primitive double array.

Parameters:

values - the primitive int array to represent.

Returns:

never code null. The returned list will be unmodifiable yet it will reflect changes in values in the original array yet you cannot change the values.

append

@SafeVarargs
public static <T> java.util.List<T> append(java.util.List<T> left,
                                                        T... elts)

Create a new list that contains the elements of left along with elements elts

Parameters:

left - a non-null list of elements

elts - a varargs vector for elts to append in order to left

Returns:

A newly allocated linked list containing left followed by elts

dupChar

public static java.lang.String dupChar(char c,
                                       int nCopies)

Create a new string that's n copies of c

Parameters:

c - the char to duplicate

nCopies - how many copies?

Returns:

a string

dupString

public static java.lang.String dupString(java.lang.String s,
                                         int nCopies)

Create a new string thats a n duplicate copies of s

Parameters:

s - the string to duplicate

nCopies - how many copies?

Returns:

a string

dupBytes

public static byte[] dupBytes(byte b,
                              int nCopies)

Create a new byte array that's n copies of b

Parameters:

b - the byte to duplicate

nCopies - how many copies?

Returns:

a byte array

countBooleanOccurrences

public static int countBooleanOccurrences(boolean element,
                                          boolean[] array)

Returns the number of occurrences of a boolean element in a boolean array.

Parameters:

element -

array - cannot be null

Returns:

escapeExpressions

public static java.lang.String[] escapeExpressions(java.lang.String args)

Splits expressions in command args by spaces and returns the array of expressions. Expressions may use single or double quotes to group any individual expression, but not both.

Parameters:

args - Arguments to parse.

Returns:

Parsed expressions.

repeatChars

public static byte[] repeatChars(char c,
                                 int n)

makes an array filled with n copies of the given char.

repeatBytes

public static byte[] repeatBytes(byte b,
                                 int n)

makes an array filled with n copies of the given byte.

makePermutations

public static <T> java.util.List<java.util.List<T>> makePermutations(java.util.List<T> objects,
                                                                     int n,
                                                                     boolean withReplacement)

Make all combinations of N size of objects if objects = [A, B, C] if N = 1 => [[A], [B], [C]] if N = 2 => [[A, A], [B, A], [C, A], [A, B], [B, B], [C, B], [A, C], [B, C], [C, C]]

Parameters:

objects - list of objects

n - size of each combination

withReplacement - if false, the resulting permutations will only contain unique objects from objects

Returns:

a list with all combinations with size n of objects.

calcMD5

public static java.lang.String calcMD5(java.lang.String s)

See Also:

calcMD5(byte[])

calcMD5

public static java.lang.String calcMD5(byte[] bytes)

Calculate the md5 for bytes, and return the result as a 32 character string

Parameters:

bytes - the bytes to calculate the md5 of

Returns:

the md5 of bytes, as a 32-character long string

calculateFileMD5

public static java.lang.String calculateFileMD5(java.io.File file)
                                         throws java.io.IOException

Calculates the MD5 for the specified file and returns it as a String

Parameters:

file - file whose MD5 to calculate

Returns:

file's MD5 in String form

Throws:

java.io.IOException - if the file could not be read

calculatePathMD5

public static java.lang.String calculatePathMD5(java.nio.file.Path path)
                                         throws java.io.IOException

Calculates the MD5 for the specified file and returns it as a String

Parameters:

path - file whose MD5 to calculate

Returns:

file's MD5 in String form

Throws:

java.io.IOException - if the file could not be read

nonNull

public static <T> T nonNull(T object)

Checks that an Object object is not null and returns the same object or throws an IllegalArgumentException

Parameters:

object - any Object

Returns:

the same object

Throws:

java.lang.IllegalArgumentException - if a o == null

nonNull

public static <T> T nonNull(T object,
                            java.lang.String message)

Checks that an Object is not null and returns the same object or throws an IllegalArgumentException

Parameters:

object - any Object

message - the text message that would be passed to the exception thrown when o == null.

Returns:

the same object

Throws:

java.lang.IllegalArgumentException - if a o == null

nonNull

public static <T> T nonNull(T object,
                            java.util.function.Supplier<java.lang.String> message)

Checks that an Object is not null and returns the same object or throws an IllegalArgumentException

Parameters:

object - any Object

message - the text message that would be passed to the exception thrown when o == null.

Returns:

the same object

Throws:

java.lang.IllegalArgumentException - if a o == null

nonEmpty

public static <I,T extends java.util.Collection<I>> T nonEmpty(T collection,
                                                               java.lang.String message)

Checks that a Collection is not null and that it is not empty. If it's non-null and non-empty it returns the input, otherwise it throws an IllegalArgumentException

Parameters:

collection - any Collection

message - a message to include in the output

Returns:

the original collection

Throws:

java.lang.IllegalArgumentException - if collection is null or empty

isNonEmpty

public static boolean isNonEmpty(java.util.Collection<?> collection)

Checks that a Collection is not null and that it is not empty. If it's non-null and non-empty it returns the true

Parameters:

collection - any Collection

Returns:

true if the collection exists and has elements

nonEmpty

public static java.lang.String nonEmpty(java.lang.String string,
                                        java.lang.String message)

Checks that a String is not null and that it is not empty. If it's non-null and non-empty it returns the input, otherwise it throws an IllegalArgumentException

Parameters:

string - any String

message - a message to include in the output

Returns:

the original string

Throws:

java.lang.IllegalArgumentException - if string is null or empty

nonEmpty

public static java.lang.String nonEmpty(java.lang.String string)

Checks that a String is not null and that it is not empty. If it's non-null and non-empty it returns the input, otherwise it throws an IllegalArgumentException

Parameters:

string - any String

Returns:

the original string

Throws:

java.lang.IllegalArgumentException - if string is null or empty

nonEmpty

public static <I,T extends java.util.Collection<I>> T nonEmpty(T collection)

Checks that a Collection is not null and that it is not empty. If it's non-null and non-empty it returns the input, otherwise it throws an IllegalArgumentException

Parameters:

collection - any Collection

Returns:

the original collection

Throws:

java.lang.IllegalArgumentException - if collection is null or empty

containsNoNull

public static void containsNoNull(java.util.Collection<?> collection,
                                  java.lang.String message)

Checks that the collection does not contain a null value (throws an IllegalArgumentException if it does).

Parameters:

collection - collection

message - the text message that would be pass to the exception thrown when c contains a null.

Throws:

java.lang.IllegalArgumentException - if collection is null or contains any null elements

checkForDuplicatesAndReturnSet

public static <E> java.util.Set<E> checkForDuplicatesAndReturnSet(java.util.Collection<E> c,
                                                                  java.lang.String message)

Checks that the collection does not contain a duplicate value (throws an IllegalArgumentException if it does). The implementation creates a Set as an intermediate step or detecting duplicates and returns this Set because it is sometimes useful to do so.

Parameters:

c - collection

message - A message to emit in case of error, in addition to reporting the first duplicate value found.

Throws:

java.lang.IllegalArgumentException - if a o == null

validIndex

public static int validIndex(int index,
                             int length)

Checks whether an index is within bounds considering a collection or array of a particular size whose first position index is 0

Parameters:

index - the query index.

length - the collection or array size.

Returns:

same value as the input index.

validIndex

public static int validIndex(int index,
                             int length,
                             java.lang.String errorMessage)

Checks whether an index is within bounds considering a collection or array of a particular size whose first position index is 0

Parameters:

index - the query index.

length - the collection or array size.

errorMessage - the error message to use in case of an exception is thrown.

Returns:

same value as the input index.

validateArg

public static void validateArg(boolean condition,
                               java.lang.String msg)

validateArg

public static void validateArg(boolean condition,
                               java.util.function.Supplier<java.lang.String> msg)

validate

public static void validate(boolean condition,
                            java.lang.String msg)

Check a condition that should always be true and throw an IllegalStateException if false. If msg is not a String literal i.e. if it requires computation, use the Supplier version, below.

validate

public static void validate(boolean condition,
                            java.util.function.Supplier<java.lang.String> msg)

Check a condition that should always be true and throw an IllegalStateException if false.

optimumHashSize

public static int optimumHashSize(int maxElements)

Calculates the optimum initial size for a hash table given the maximum number of elements it will need to hold. The optimum size is the smallest size that is guaranteed not to result in any rehash/table-resize operations.

Parameters:

maxElements - The maximum number of elements you expect the hash table will need to hold

Returns:

The optimum initial size for the table, given maxElements

equalRange

public static boolean equalRange(byte[] left,
                                 int leftOffset,
                                 byte[] right,
                                 int rightOffset,
                                 int length)

Compares sections from to byte arrays to verify whether they contain the same values.

Parameters:

left - first array to compare.

leftOffset - first position of the first array to compare.

right - second array to compare.

rightOffset - first position of the second array to compare.

length - number of positions to compare.

Returns:

true iff length is 0 or all the bytes in both ranges are the same two-by-two.

Throws:

java.lang.IllegalArgumentException - if

• either left or right is null or
• any off the offset or length combine point outside any of the two arrays

skimArray

public static <T> T skimArray(T original,
                              boolean[] remove)

Skims out positions of an array returning a shorter one with the remaning positions in the same order.

Type Parameters:

T - the array type.

Parameters:

original - the original array to splice.

remove - for each position in original indicates whether it should be spliced away (true), or retained (false)

Returns:

never null.

Throws:

java.lang.IllegalArgumentException - if either original or remove is null, or remove length is different to {@code original}'s, or original is not in fact an array.

skimArray

public static <T> T skimArray(T source,
                              int sourceOffset,
                              T dest,
                              int destOffset,
                              boolean[] remove,
                              int removeOffset)

Skims out positions of an array returning a shorter one with the remaining positions in the same order.

If the dest array provide is not long enough a new one will be created and returned with the same component type. All elements before destOffset will be copied from the input to the result array. If dest is null, a brand-new array large enough will be created where the position preceding destOffset will be left with the default value. The component type Will match the one of the source array.

Type Parameters:

T - the array type.

Parameters:

source - the original array to splice.

sourceOffset - the first position to skim.

dest - the destination array.

destOffset - the first position where to copy the skimmed array values.

remove - for each position in original indicates whether it should be spliced away (true), or retained (false)

removeOffset - the first position in the remove index array to consider.

Returns:

never null.

Throws:

java.lang.IllegalArgumentException - if either original or remove is null, or remove length is different to {@code original}'s, or original is not in fact an array.

skimArray

public static <T> T skimArray(T source,
                              int sourceOffset,
                              T dest,
                              int destOffset,
                              boolean[] remove,
                              int removeOffset,
                              int length)

Skims out positions of an array returning a shorter one with the remaning positions in the same order.

If the dest array provide is not long enough a new one will be created and returned with the same component type. All elements before destOffset will be copied from the input to the result array. If dest is null, a brand-new array large enough will be created where the position preceding destOffset will be left with the default value. The component type Will match the one of the source array.

Type Parameters:

T - the array type.

Parameters:

source - the original array to splice.

sourceOffset - the first position to skim.

dest - the destination array.

destOffset - the first position where to copy the skimed array values.

remove - for each position in original indicates whether it should be spliced away (true), or retained (false)

removeOffset - the first position in the remove index array to consider.

length - the total number of position in source to consider. Thus only the sourceOffset to sourceOffset + length - 1 region will be skimmed.

Returns:

never null.

Throws:

java.lang.IllegalArgumentException - if either original or remove is null, or remove length is different to {@code original}'s, or original is not in fact an array.

warnOnNonIlluminaReadGroups

public static void warnOnNonIlluminaReadGroups(htsjdk.samtools.SAMFileHeader readsHeader,
                                               org.apache.logging.log4j.Logger logger)

Checks if the read header contains any reads groups from non-Illumina and issue a warning of that's the case.

xor

public static boolean xor(boolean x,
                          boolean y)

Boolean xor operation. Only true if x != y.

Parameters:

x - a boolean

y - a boolean

Returns:

true if x != y

lastIndexOf

public static int lastIndexOf(byte[] reference,
                              byte[] query)

Find the last occurrence of the query sequence in the reference sequence Returns the index of the last occurrence or -1 if the query sequence is not found

Parameters:

reference - the reference sequence

query - the query sequence

listFromPrimitives

public static java.util.List<java.lang.Integer> listFromPrimitives(int[] ar)

Simple wrapper for sticking elements of a int[] array into a List

Parameters:

ar - - the array whose elements should be listified

Returns:

- a List where each element has the same value as the corresponding index in @ar

concatIterators

public static <T> java.util.Iterator<T> concatIterators(java.util.Iterator<? extends java.lang.Iterable<T>> iterator)

Concatenates a series of Iterators (all of the same type) into a single Iterator.

Type Parameters:

T - the type of the iterator

Parameters:

iterator - an Iterator of Iterators

Returns:

an Iterator over the underlying Iterators

stream

public static <T> java.util.stream.Stream<T> stream(java.util.Enumeration<T> enumeration)

stream

public static <T> java.util.stream.Stream<T> stream(java.lang.Iterable<T> iterable)

stream

public static <T> java.util.stream.Stream<T> stream(java.util.Iterator<T> iterator)

identityFunction

public static <T> java.util.function.Function<T,T> identityFunction()

Returns a function that always returns its input argument. Unlike Function.identity() the returned function is also serializable.

Type Parameters:

T - the type of the input and output objects to the function

Returns:

a function that always returns its input argument

transformParallel

public static <F,T> java.util.Iterator<T> transformParallel(java.util.Iterator<F> fromIterator,
                                                            java.util.function.Function<F,T> function,
                                                            int numThreads)

Like Guava's Iterators.transform(Iterator, com.google.common.base.Function), but runs a fixed number (numThreads) of transformations in parallel, while maintaining ordering of the output iterator. This is useful if the transformations are CPU intensive.

getDuplicatedItems

public static <T> java.util.Set<T> getDuplicatedItems(java.util.Collection<T> objects)

Gets duplicated items in the collection.

getDateTimeForDisplay

public static java.lang.String getDateTimeForDisplay(java.time.ZonedDateTime dateTime)

Return the given dateTime formatted as string for display.

Parameters:

dateTime - the date/time to be formatted

Returns:

String representing the dateTime.

forceJVMLocaleToUSEnglish

public static void forceJVMLocaleToUSEnglish()

Set the Locale to US English so that numbers will always be formatted in the US style.

getMedianValue

public static <T extends java.lang.Comparable<?>> T getMedianValue(java.util.List<T> values)

Streams and sorts a collection of objects and returns the integer median entry of the sorted list

Parameters:

values - List of sortable entries from which to select the median

split

public static java.util.List<java.lang.String> split(java.lang.String str,
                                                     char delimiter)

Splits a String using indexOf instead of regex to speed things up. This method produces the same results as String.split(String) and String.split(String, 0), but has been measured to be ~2x faster (see StringSplitSpeedUnitTest for details).

Parameters:

str - the string to split.

delimiter - the delimiter used to split the string.

Returns:

A List of String tokens.

split

public static java.util.List<java.lang.String> split(java.lang.String str,
                                                     java.lang.String delimiter)

Splits a String using indexOf instead of regex to speed things up. If given an empty delimiter, will return each character in the string as a token. This method produces the same results as String.split(String) and String.split(String, 0), but has been measured to be ~2x faster (see StringSplitSpeedUnitTest for details).

Parameters:

str - the string to split.

delimiter - the delimiter used to split the string.

Returns:

A List of String tokens.

getReverseValueToListMap

public static <T,U> java.util.Map<U,java.util.Set<T>> getReverseValueToListMap(java.util.Map<T,java.util.List<U>> somethingToListMap)

Take a map of a value to a list and reverse it. Note that no assumptions of uniqueness are made, so returned values are also lists.

For example:

Input:
k -> {a,b}
j -> {a}
Output:
a -> {k,j}
b -> {k}
Any sorting in the input map will be lost in the output.

Type Parameters:

T - class of the key of the input

U - class of the values in the list of the input

Parameters:

somethingToListMap - a map from a value to a list of values. Never null

Returns:

A new mapping from class of values to set of keys. Never null

formattedPercent

public static java.lang.String formattedPercent(long x,
                                                long total)

Convenience function that formats a percentage as a %.2f string

Parameters:

x - number of objects part of total that meet some criteria

total - count of all objects, including x

Returns:

a String percent rate, or NA if total == 0

formattedRatio

public static java.lang.String formattedRatio(long num,
                                              long denom)

Convenience function that formats a ratio as a %.2f string

Parameters:

num - number of observations in the numerator

denom - number of observations in the denumerator

Returns:

a String formatted ratio, or NA if all == 0

filterCollectionByExpressions

public static java.util.Set<java.lang.String> filterCollectionByExpressions(java.util.Collection<java.lang.String> sourceValues,
                                                                            java.util.Collection<java.lang.String> filterExpressions,
                                                                            boolean exactMatch)

Given a collection of strings and a collection of regular expressions, generates the set of strings that match any expression

Parameters:

sourceValues - collection of strings from which to to select

filterExpressions - list of expressions to use for matching

exactMatch - If true match filters exactly, otherwise use as both exact and regular expressions

Returns:

A new set strings from sourceValues that satisfy at least one of the expressions in sampleExpressions

runInParallel

public static <T> T runInParallel(int threads,
                                  java.util.function.Supplier<T> supplier)

Runs a task in parallel returning it returned result.

This call will wait until such task is completed.

Type Parameters:

T - the type of the return.

Parameters:

threads - number of threads requested. 0 would result in using a system default, usually the host number of CPU cores.

supplier - the task to run.

Returns:

whatever the input task returns in the end, it can be null.

Throws:

GATKException - if the run was interrupted or resulted in a checked exception. Unchecked exceptions and Error progragate as they are.