org.broadinstitute.hellbender.tools.spark.sv.utils

Class SVUtils

java.lang.Object

org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils

public final class SVUtils
extends java.lang.Object

Useful scraps of this and that.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SVUtils.IteratorFilter<T>

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	GATKSV_CONTIG_ALIGNMENTS_READ_GROUP_ID

Constructor Summary

Constructors

Constructor and Description
SVUtils()

Method Summary

Modifier and Type	Method and Description
static <T> java.util.stream.Collector<T,?,java.util.ArrayList<T>>	arrayListCollector(int size) Provides a stream collector that will collect items into an array list with a given initial capacity.
static <T> java.util.List<T>	concatenateLists(java.util.List<T> list1, java.util.List<T> list2) Concatenate two lists.
static long	fnvByteArray64(byte[] toHash) 64-bit FNV-1a hash for byte arrays
static long	fnvByteArray64(long start, byte[] toHash)
static long	fnvLong64(long toHash) 64-bit FNV-1a hash for long's
static long	fnvLong64(long start, long toHash)
static java.util.List<java.lang.String>	getAttributeAsStringList(htsjdk.variant.variantcontext.VariantContext vc, java.lang.String attributeKey) todo: this should be fixed in a new major version of htsjdk this exist because for whatever reason, VC.getAttributeAsStringList() sometimes returns a giant single string, while using VC.getAttributeAsString() gives back an array.....
static java.util.stream.Stream<java.lang.String>	getAttributeAsStringStream(htsjdk.variant.variantcontext.VariantContext vc, java.lang.String attributeKey)
static java.util.Set<java.lang.String>	getCanonicalChromosomes(java.lang.String nonCanonicalContigNamesFile, htsjdk.samtools.SAMSequenceDictionary dictionary) Canonical chromosomes are defined, for homo sapiens, as chromosomes 1-22, chromosome X and Y.
static java.lang.String	getSampleId(htsjdk.samtools.SAMFileHeader header)
static htsjdk.samtools.SAMRecordComparator	getSamRecordComparator(htsjdk.samtools.SAMFileHeader.SortOrder sortOrder) Given sortOrder, provide appropriate comparator.
static <T extends java.lang.Enum<T>> java.util.EnumMap<T,java.lang.Long>	getZeroInitializedEnumMap(java.lang.Class<T> clazz)
static int	hashMapCapacity(int nElements) return a good initialCapacity for a HashMap that will hold a given number of elements
static <T> int	iteratorSize(java.util.Iterator<T> itr) count the number of items available from an iterator
static int	iteratorSize(LongIterator itr)
static SimpleInterval	makeOneBpInterval(java.lang.String chr, int pos) Given chromosome name and requested position (1-based coordinate system), return a 1 bp long interval that spans only the requested base.
static <T> java.util.Iterator<T>	singletonIterator(T t)
static java.util.Collection<SVKmer>	uniquify(java.util.Collection<SVKmer> coll1, java.util.Collection<SVKmer> coll2)

Methods inherited from class java.lang.Object

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

Field Detail

GATKSV_CONTIG_ALIGNMENTS_READ_GROUP_ID

public static final java.lang.String GATKSV_CONTIG_ALIGNMENTS_READ_GROUP_ID

See Also:

Constant Field Values

Constructor Detail

SVUtils

public SVUtils()

Method Detail

getSampleId

public static java.lang.String getSampleId(htsjdk.samtools.SAMFileHeader header)

getSamRecordComparator

public static htsjdk.samtools.SAMRecordComparator getSamRecordComparator(htsjdk.samtools.SAMFileHeader.SortOrder sortOrder)

Given sortOrder, provide appropriate comparator. Currently only support coordinate or query-name order, and throws UserException if other values are specified.

getAttributeAsStringList

public static java.util.List<java.lang.String> getAttributeAsStringList(htsjdk.variant.variantcontext.VariantContext vc,
                                                                        java.lang.String attributeKey)

todo: this should be fixed in a new major version of htsjdk this exist because for whatever reason, VC.getAttributeAsStringList() sometimes returns a giant single string, while using VC.getAttributeAsString() gives back an array.....

getAttributeAsStringStream

public static java.util.stream.Stream<java.lang.String> getAttributeAsStringStream(htsjdk.variant.variantcontext.VariantContext vc,
                                                                                   java.lang.String attributeKey)

makeOneBpInterval

public static SimpleInterval makeOneBpInterval(java.lang.String chr,
                                               int pos)

Given chromosome name and requested position (1-based coordinate system), return a 1 bp long interval that spans only the requested base.

getCanonicalChromosomes

public static java.util.Set<java.lang.String> getCanonicalChromosomes(java.lang.String nonCanonicalContigNamesFile,
                                                                      @Nonnull
                                                                      htsjdk.samtools.SAMSequenceDictionary dictionary)

Canonical chromosomes are defined, for homo sapiens, as chromosomes 1-22, chromosome X and Y.

hashMapCapacity

public static int hashMapCapacity(int nElements)

return a good initialCapacity for a HashMap that will hold a given number of elements

iteratorSize

public static <T> int iteratorSize(java.util.Iterator<T> itr)

count the number of items available from an iterator

iteratorSize

public static int iteratorSize(LongIterator itr)

singletonIterator

public static <T> java.util.Iterator<T> singletonIterator(T t)

uniquify

public static java.util.Collection<SVKmer> uniquify(java.util.Collection<SVKmer> coll1,
                                                    java.util.Collection<SVKmer> coll2)

concatenateLists

public static <T> java.util.List<T> concatenateLists(java.util.List<T> list1,
                                                     java.util.List<T> list2)

Concatenate two lists.

arrayListCollector

public static <T> java.util.stream.Collector<T,?,java.util.ArrayList<T>> arrayListCollector(int size)

Provides a stream collector that will collect items into an array list with a given initial capacity.

getZeroInitializedEnumMap

public static <T extends java.lang.Enum<T>> java.util.EnumMap<T,java.lang.Long> getZeroInitializedEnumMap(java.lang.Class<T> clazz)

fnvLong64

public static long fnvLong64(long toHash)

64-bit FNV-1a hash for long's

fnvLong64

public static long fnvLong64(long start,
                             long toHash)

fnvByteArray64

public static long fnvByteArray64(byte[] toHash)

64-bit FNV-1a hash for byte arrays

fnvByteArray64

public static long fnvByteArray64(long start,
                                  byte[] toHash)