SequenceFormats.VCF

A module to help with parsing VCF files. The VCF format is defined here: https://en.wikipedia.org/wiki/Variant_Call_Format

Documentation

data VCFheader

A datatype to represent the VCF Header. Most comments are simply parsed as entire lines, but the very last comment line, containing the sample names, is separated out

Constructors

VCFheader

Fields

• vcfHeaderComments :: [String]

  A list of containing all comments starting with a single #

• vcfSampleNames :: [String]

  The list of sample names parsed from the last comment line starting with ##

Instances

Show VCFheader

Defined in SequenceFormats.VCF

Methods

showsPrec :: Int -> VCFheader -> ShowS

show :: VCFheader -> String

showList :: [VCFheader] -> ShowS

data VCFentry

A Datatype representing a single VCF entry.

Constructors

VCFentry

Fields

• vcfChrom :: Chrom

  The chromosome

• vcfPos :: Int

  The position

• vcfId :: Maybe ByteString

  The SNP ID if non-missing

• vcfRef :: ByteString

  The reference allele (supports also multi-character alleles for Indels)

• vcfAlt :: [ByteString]

  The alternative alleles, each one possible of multiple characters

• vcfQual :: Maybe Double

  The quality value

• vcfFilter :: Maybe ByteString

  The Filter value, if non-missing.

• vcfInfo :: [ByteString]

  A list of Info fields

• vcfFormatString :: [ByteString]

  A list of format tags

• vcfGenotypeInfo :: [[ByteString]]

  A list of format fields for each sample.

Instances

Show VCFentry

Defined in SequenceFormats.VCF

Methods

showsPrec :: Int -> VCFentry -> ShowS

show :: VCFentry -> String

showList :: [VCFentry] -> ShowS

Eq VCFentry

Defined in SequenceFormats.VCF

Methods

(==) :: VCFentry -> VCFentry -> Bool

(/=) :: VCFentry -> VCFentry -> Bool

Genomic VCFentry

Defined in SequenceFormats.Genomic

Methods

genomicPosition :: VCFentry -> (Chrom, Int)

genomicChrom :: VCFentry -> Chrom

genomicBase :: VCFentry -> Int

readVCFfromStdIn :: (MonadIO m, MonadThrow m) => m (VCFheader, Producer VCFentry m ())

Reading a VCF from StdIn. Returns a VCFHeader and a Producer over VCFentries.

readVCFfromFile :: MonadSafe m => FilePath -> m (VCFheader, Producer VCFentry m ())

Reading a VCF from a file. Returns a VCFHeader and a Producer over VCFentries.

getGenotypes :: VCFentry -> Either String [ByteString]

Extracts the genotype fields (for each sapmle) from a VCF entry

getDosages :: VCFentry -> Either String [Maybe Int]

Extracts the dosages (the sum of non-reference alleles) per sample (returns a Left Error if it fails.)

isTransversionSnp :: ByteString -> [ByteString] -> Bool

returns True if the SNp is a biallelic Transversion SNP (i.e. one of GT, GC, AT, AC)

vcfToFreqSumEntry :: VCFentry -> Either String FreqSumEntry

Converts a VCFentry to the simpler FreqSum format (returns a Left Error if it fails.)

isBiallelicSnp :: ByteString -> [ByteString] -> Bool

returns True if the SNP is biallelic.