read.pyRAD: Read in data from pyRAD
In RADami: Phylogenetic Analysis of RADseq Data

Description Usage Arguments Details Value Author(s) See Also

This function begins essentially all analyses in this package. It reads in the pyRAD loci file and stores it in a form to facilitate a variety of downstream analyses coded in this package.

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read.pyRAD(filename, reportInterval = 20000,
	         breakLinesSeparate = FALSE, 
           doSummary = TRUE, ...)

`filename`	name of the pyRAD loci file
`reportInterval`	how often to report progress while reading and processing files
`breakLinesSeparate`	are there separate break lines (blank) and summary lines (not blank) between loci in the pyRAD file?
`doSummary`	should `summary.pyRAD.loci` be run on the object and appended to the end?
`...`	extra arguments to be passed along to `readLines`

As written, this function has a lot of summary embedded in it. The default doSummary = TRUE should be left for the other higher-level functions to work properly

A list with the following items:

`tips`	a character vector of the tips for each sequence
`seqs`	a character vector of all sequences
`breaks`	an integer vector indexing the lines that are breaks between loci
`break.vectors`	a named character vector of the break lines between vectors, with names corresponding to locus names
`cons`	a named character vector of the lines summarizing each locus, with names corresponding to locus names; if `breakLinesSeparate = F`, this is identical to `break.vectors`
`locus.index`	an index corresponding to `seqs` and `tips`, indicating what locus each belongs to
`file.read`	name of the file read in
`timestamp`	timestamp for exiting the function
`radSummary`	an object of class `summary.pyRAD.loci`, if called, which it is by default