Data Structures

Here are the data structures with brief descriptions:

Allele	Summary statistics from the allele command
Args	Struct to pass around command line arguments. Will either be depricated, or will be integreated into the interface.h*/
Argument	A command line argument. See the interface tutorial for a demonstration of usage
Base	A class converts human readable bases to bit flags
Base_file	A templet which stores data associated with specific locations in a genome
Bcf2pro	Because of the god awful mess that are vcf header lines
Bcf2pro_file	Because of the god awful mess that are vcf header lines
Bed_data
Bed_file
binomial	A class that returns the binomial coefficient or the pdf the binomial distribution. Not Log
Command	A sub-command of mapgd
Constants
Data	A class which can be written as flat text file or into an SQL database
Data_file
Double_indexed_data
Double_indexed_file
Environment	A class for handling options and automatically formating –help, -h, -u and -v
External_data	An interface used to read/write data from outside of mapgd
External_file	An interface for reading and writing data specified outside of mapgd
File_index	An interface that transforms pairs of name and position keys into record numbers
file_s
Flag	A class that passes command line flags. It takes no arguments and chews only a single letter.*/
Flat_file
Genotype
Genotype_pair
gzstreambase
gzstreambuf
igzstream
Indexed_data	Data which has an absolute position
Indexed_file
Info	Because of the god awful mess that are vcf header lines
Key	A key is (i.e. what the user called it)
Linkage	A class to store linkage information
lnmultinomial
Locus
Log	A class to store a log of commands that have been run
models
ogzstream
Pedigree	Pedigree data
Pedigree_record
Phenotype	Phenotype data
Plink_data
Plink_file
Plink_record
Pooled_data	Information genereated from pooled data
Population	Population genotypes
quartet	A class that stores quartet information
Region
Registration	A class which registers a child of Data in Data::new_data_
Relatedness	Relatedness data
Sample_gof	The sample specific goodness of fit
Sample_name	The name of a sample (i.e. what the user called it)
small_rel
sort_second
State
State_stream
Tmp_buffer
Tmp_streambuf
Vcf_data
Vcf_file