|Class||Data Declaration command|
|Arguments||<map file name> [[k]bp]|
Read in map positions for loci from a file, matching via names of previously declared markers. Should recognize most formats of map file automatically eg GVF, Merlin, Mendel, Solar. Tests for identifier strings in the header (notably GVF), then checks number of columns and whether column contents are numeric or alphabetical, skipping first row as possible header. The bp (kbp) modifier tells Sib-pair to divide the positions by 106 (103); thus the map distances become Mbp, and remain readable.
>> read loc merlin merlin.dat
Read in names of 5 loci from locus file.
>> read map merlin.map
Matched up 4 loci with their map positions.
>> read map Homo_sapiens.gvf.gz
Matched up 2999789 loci with their map positions.
|set map <pos1>...<posN>||set marker map|
|show map||show linkage map|
|<< (set chromosomes)||Up to index||>> (read chain)|