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# NAME: OPTIONS
# VERSION: 2.0.0a17 (13MAY2005)
# AUTHOR: John B. Cole, PhD (jcole@aipl.arsusda.gov)
# LICENSE: LGPL
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# This file lists the options that can be used in PyPedal programs.  Options
# control things such as pedigree formats and output filenames.
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Option          Default     Note(s)
------          -------     -------
pedfile         None        File from which pedigree is read; must provide.
pedformat       'asd'       See PEDIGREE_FORMAT_CODES for details.
pedname         'Untitled'  A name/title for your pedigree.
messages        'verbose'   How many message should PyPedal provide;
                            only 'verbose' is currently implemented.
renumber        0           Renumber the pedigree after reading from file (0/1).
set_generations 0           Iterate over the pedigree to infer generations (0/1).
set_ancestors   0           Iterate over the pedigree to assign ancestors lists to
                            parents in the pedigree (0/1).
set_alleles     0           Assign alleles for use in gene-drop simulations (0/1).
sepchar         ' '         The character separating columns of input in the
                            pedfile.
alleles_sepchar '/'         The character separating the two alleles in an
                            animal's allelotype.  'alleles_sepchar' must NOT be
                            the same as 'sepchar'!
counter         1000        How often should PyPedal write a progress message to
                            the screen when reading large pedigree files.
slow_reorder    1           Option to override the slow, but more-correct,
                            reordering routine used by PyPedal  by default (0/1).
                            ONLY CHANGE THIS IF YOU REALLY UNDERSTAND WHAT IT
                            DOES!  Careless use of this option can lead to
                            erroneous results.
filetag         pedfile     A filetag is a descriptive label attached to output files
                            created when processing a pedigree.  By default the
                            filetag is based on 'pedfile', minus its file
                            extension.
logfile         filetag.log The name of the file to which PyPedal should write messages
                            about its progress.
missing_parent  '0'         Indicates what code is used to identify
                            missing/unknown parents in the pedigree file.
file_io         1           When true, routines that can write results to output
                            files will do so and put messages in the program log
                            to that effect.
debug_messages  0           Indicates whether or not PyPedal should print
                            debugging information.
pedigree_is_renumbered   0  Indicates whether or not the pedigree is
                            already renumbered.  If renumber
                            is set to '1' that setting will override
                            pedigree_is_renumbered.
form_nrm                 0  Indicates whether or not to form a NRM and attach it
                            to the current pedigree object.  WARNING: if you are
                            working with a very large pedigree this may cause
                            problems depending on the maount of RAM your system
                            has.
nrm_method            'nrm' Indicates which method should be used to form the NRM.
                            By default the NRM is formed using the tabular method
                            with no correction for parental inbreeding.  To correct
                            for parental inbreeding use 'frm'.