Detailed Description

SNP table data format.

This class is used to deal with simple "polymorphism tables" that are formatted in a particular way.

The major purpose of this class is to be able to read in data files in this format. An example of the format is as follows:

6 6
679 1004 1153 1155 1277 1295
N N N N N N
Sim2 A C C G A A
Sim3 G C T G A C
Sim4 A C C T G C
Sim5 A C C T G C
Sim7 A T C T A C
Sim8 A C C G A A

The two numbers on the first line are the sample size and number of segregating sites, respectively. The next line contains the positions of each site. The third line contains the outgroup state for each variable site–if this is unknown, use an 'N' to indicate the ambiguity. The rest of the lines contain a unique sequence name, and then the states of each segregating site.

Finally, if all of the outgroup states are missing (as is the case in the above example, then it is assumed that no outgroup was typed, and no outgroup sequence is stored in PolyTable::data. However, if at least one of the outgroup states is unambiguous, a std::string representing outgroup states is stored as the first element in PolyTable::data.

The documentation for this class was generated from the following file:

SimpleSNP.hpp