import_IBD: Import IBD probabilities as estimated by TetraOrigin
In polyqtlR: QTL Analysis in Autopolyploid Bi-Parental F1 Populations

Imports the summarised IBD probability output of TetraOrigin (which estimates IBD probabilities at all marker positions), and interpolates these at a grid of positions at user-defined spacing.

import_IBD(
  folder = NULL,
  filename.vec,
  bivalent_decoding = TRUE,
  error = 0.01,
  log = NULL
)

`folder`	The path to the folder in which the TetraOrigin output is contained, default is `NULL` if files are in working directory.
`filename.vec`	A vector of the character filename(s) of the `.csv` file(s) containing the output of TetraOrigin. Should be in order according to LG/chromosome numbering.
`bivalent_decoding`	Logical, if `TRUE` then only bivalent pairing was allowed in TetraOrigin, specify `FALSE` if multivalent pairing was also allowed.
`error`	The offspring error prior used in the offspring decoding step, here assumed to be 0.01
`log`	Character string specifying the log filename to which standard output should be written. If `NULL` log is send to stdout.

Returns a list with the following items:

`IBDtype :`	Always "genotypeIBD" for the output of TetraOrigin
`IBDarray :`	An array of IBD probabilities. The dimensions of the array are: markers, genotype classes and individuals.
`map :`	Integrated linkage map positions of markers used in IBD calculation
`parental_phase :`	The parental marker phasing as used by TetraOrigin, recoded in 1 and 0's
`marginal.likelihoods :`	A list of marginal likelihoods of different valencies, currently `NULL`
`valency :`	The predicted valency that maximised the marginal likelihood, per offspring. Currently `NULL`
`offspring :`	Offspring names
`biv_dec :`	Logical, the bivalent_decoding parameter specified.
`gap :`	The gap size used in IBD interpolation, by default `NULL`. See `spline_IBD`
`genocodes :`	Ordered list of genotype codes used to represent different genotype classes.
`pairing :`	log likelihoods of each of the different pairing scenarios considered (can be used e.g. for post-mapping check of preferential pairing)
`ploidy :`	The ploidy of parent 1, by default assumed to be 4
`ploidy2 :`	The ploidy of parent 2, by default assumed to be 4
`method :`	The method used, always returned as "hmm_TO" (Hidden Markov Model TetraOrigin)
`error :`	The error prior used in the calculation, assumed to be 0.01