vcf

Type Members

implicit class BiopetGenotype extends AnyRef
implicit class BiopetVariantContext extends AnyRef
class GeneralStats extends Serializable

This class will collect general stats from vcf records
class GenotypeFieldCounts extends Serializable

This class will track all values of 1 genotype field
class GenotypeStats extends Serializable

This class will collect general stats from vcf records
class InfoFieldCounts extends Serializable

This class will track all possible value of a single INFO field
class SampleCompare extends Serializable

This class can record overlapping alleles and genotypes
class SampleDistributions extends Serializable
case class VcfField(key: String, method: FieldMethod.Value) extends Product with Serializable

Value Members

object FieldMethod extends Enumeration
object GeneralStats extends Enumeration

Enum to store methods
object GenotypeStats extends Enumeration

Enum to store methods
object VcfField extends Serializable
def alleleIndexOverlap(g1: List[Int], g2: List[Int], start: Int = 0): Int

Give back the number of alleles that overlap
def alleleOverlap(g1: List[Allele], g2: List[Allele], start: Int = 0): Int

Give back the number of alleles that overlap
def fillAllele(bases: String, newSize: Int, fillWith: Char = '-'): String

Method will extend a allele till a new length
Method will extend a allele till a new length
bases
Allele
newSize
New size of allele
fillWith
Char to fill gap
def getSampleIds(vcf: File): List[String]

Get sample IDs from vcf File
Get sample IDs from vcf File
vcf
File object pointing to vcf
returns
list of strings with sample IDs
def getVcfIndexFile(vcfFile: File): File
def isBlockGVcf(header: VCFHeader): Boolean

Return true if header is a block-type GVCF file
Return true if header is a block-type GVCF file
header
header of Vcf file
returns
boolean
def loadRegion(reader: VCFFileReader, region: BedRecord): Iterator[VariantContext]

Returns a iterator for records from region
Returns a iterator for records from region
reader
reader to use
region
Region to fetch
def loadRegion(inputFile: File, region: BedRecord): Seq[VariantContext]

Read all records of a single regions
Read all records of a single regions
inputFile
input vcf file
region
Region to fetch
returns
Vcf records
def loadRegions(inputFile: File, regions: Iterator[BedRecord]): Iterator[VariantContext] with AutoCloseable

This method will return multiple region as a single iterator
This method will return multiple region as a single iterator
inputFile
input vcf file
regions
regions to fetch, if regions does overlap
def vcfFileIsEmpty(file: File): Boolean

Deprecated Value Members

def scalaListToJavaObjectArrayList(array: List[Any]): ArrayList[AnyRef]

Deprecated
Moved to nl.biopet.utils.conversions

package vcf

Type Members

implicit class BiopetGenotype extends AnyRef

implicit class BiopetVariantContext extends AnyRef

class GeneralStats extends Serializable

class GenotypeFieldCounts extends Serializable

class GenotypeStats extends Serializable

class InfoFieldCounts extends Serializable

class SampleCompare extends Serializable

class SampleDistributions extends Serializable

case class VcfField(key: String, method: FieldMethod.Value) extends Product with Serializable

Value Members

object FieldMethod extends Enumeration

object GeneralStats extends Enumeration

object GenotypeStats extends Enumeration

object VcfField extends Serializable

def alleleIndexOverlap(g1: List[Int], g2: List[Int], start: Int = 0): Int

def alleleOverlap(g1: List[Allele], g2: List[Allele], start: Int = 0): Int

def fillAllele(bases: String, newSize: Int, fillWith: Char = '-'): String

def getSampleIds(vcf: File): List[String]

def getVcfIndexFile(vcfFile: File): File

def isBlockGVcf(header: VCFHeader): Boolean

def loadRegion(reader: VCFFileReader, region: BedRecord): Iterator[VariantContext]

def loadRegion(inputFile: File, region: BedRecord): Seq[VariantContext]

def loadRegions(inputFile: File, regions: Iterator[BedRecord]): Iterator[VariantContext] with AutoCloseable

def vcfFileIsEmpty(file: File): Boolean

Deprecated Value Members

def scalaListToJavaObjectArrayList(array: List[Any]): ArrayList[AnyRef]

Inherited from AnyRef

Inherited from Any

Ungrouped