Every line is an individual present in DEME_ID. Genotypes of individual's chromosomes are encoded in columns CH1, CH2, ... CHn, where n is number of chromosomes. Where each genotype CHi is encoded by sizes of blocks starting always by A block. For example an individual in deme with ID 2 with 3 chromosomes and 10 loci per chromosome
2 3,5,2 10 0,9,1
have genotypes 'AAABBBBBAA AAAAAAAAAA BBBBBBBBBA'.
This format have several implicit properties:
number of rows is equal to total number of individuals in simulation
number of columns is number of chromosomes + 1
number of blocks per chromosome is equal to number of non-zero elements
A blocks have always even positions in encoding, B blocks have always odd positions
Sidenote for me: once this issue is close (format implemented), this text should be added to wiki
The current block format described in wiki/outputs is very hard to read.
After discussion with @StuartJEBaird we have decided to reformat it to tsv file:
Every line is an individual present in
DEME_ID
. Genotypes of individual's chromosomes are encoded in columnsCH1, CH2, ... CHn
, wheren
is number of chromosomes. Where each genotypeCHi
is encoded by sizes of blocks starting always byA
block. For example an individual in deme with ID 2 with 3 chromosomes and 10 loci per chromosomehave genotypes 'AAABBBBBAA AAAAAAAAAA BBBBBBBBBA'.
This format have several implicit properties:
Sidenote for me: once this issue is close (format implemented), this text should be added to wiki