TODO: Import.

• The Counts Format

The input of PoMo is allele frequency data. Especially, when populations have many individuals it is preferable to count the number of bases at each position. This decreases file size and speeds up the parser.

Counts files contain:

• One headerline that specifies the file as counts file and states the number of populations as well as the number of sites (separated by white space).
• A second headerline with white space separated headers: CRHOM (chromosome), POS (position) and sequence names.
• Many lines with counts of A, C, G and T bases and their respective positions.

Comments:

• Lines starting with # before the first headerline are treated as comments.

A toy example:

    COUNTSFILE  NPOP 5   NSITES N
    CHROM  POS  Sheep    BlackSheep  RedSheep  Wolf     RedWolf
    1      1    0,0,1,0  0,0,1,0     0,0,1,0   0,0,5,0  0,0,0,1
    1      2    0,0,0,1  0,0,0,1     0,0,0,1   0,0,0,5  0,0,0,1
    .
    .
    .
    9      8373 0,0,0,1  1,0,0,0     0,1,0,0   0,1,4,0  0,0,1,0
    .
    .
    .
    Y      9999 0,0,0,1  0,1,0,0     0,1,0,0   0,5,0,0  0,0,1,0