SequenceFormats.RareAlleleHistogram

A module to read and write allele sharing histograms, as defined here: https://rarecoal-docs.readthedocs.io/en/latest/rarecoal.html#histogram-files

Documentation

data RareAlleleHistogram

A datatype to represent an Allele Sharing Histogram:

Constructors

RareAlleleHistogram

Fields

• raNames :: [String]

  A list of branch names

• raNVec :: [Int]

  A list of haploid sample sizes.

• raMinAf :: Int

  The minimum allele count

• raMaxAf :: Int

  The maximum allele count

• raConditionOn :: [Int]

  A list of branch indices that were used to condition the allele sharing pattern

• raExcludePatterns :: [SitePattern]

  A list of patterns that are excluded.

• raTotalNrSites :: Int64

  The total number of non-missing sites in the genome.

• raCounts :: Map SitePattern Int64

  The actual data, a dictionary from allele sharing patterns to observed numbers.

• raJackknifeEstimates :: Maybe (Map SitePattern (Double, Double))

  An optional dictionary that contains Jackknife estimates and standard deviations for each pattern frequency.

Instances

Show RareAlleleHistogram

Defined in SequenceFormats.RareAlleleHistogram

Methods

showsPrec :: Int -> RareAlleleHistogram -> ShowS

show :: RareAlleleHistogram -> String

showList :: [RareAlleleHistogram] -> ShowS

Eq RareAlleleHistogram

Defined in SequenceFormats.RareAlleleHistogram

Methods

(==) :: RareAlleleHistogram -> RareAlleleHistogram -> Bool

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

readHistogramFromHandle :: MonadIO m => Handle -> m RareAlleleHistogram

Read a histogram from a File Handle.

type SitePattern = [Int]

A simple type synonym for the SitePattern, represented as a list of Integers that represents each pattern across the branches.

readHistogram :: MonadIO m => FilePath -> m RareAlleleHistogram

Read a histogram from a FilePath

writeHistogramStdOut :: MonadIO m => RareAlleleHistogram -> m ()

Write a histogram to the stdout

writeHistogramFile :: MonadIO m => FilePath -> RareAlleleHistogram -> m ()

Write a histogram to a file

showSitePattern :: SitePattern -> String

A simple function to convert a pattern into a String.