# create_marker_index
#
# find marker names in map and create index of locations
# (indexes start at 0)
create_marker_index <-
function(marker_names, map)
{
if(length(marker_names) != length(map))
stop("Different numbers of chromosomes")
if(!all(names(marker_names) == names(map)))
stop("Different chromosome names")
index <- vector("list", length(map))
for(i in seq(along=marker_names)) {
if(!all(marker_names[[i]] %in% names(map[[i]])))
stop("Some markers not found in map")
index[[i]] <- match(names(map[[i]]), marker_names[[i]]) - 1
index[[i]][is.na(index[[i]])] <- -1
}
names(index) <- names(map)
index
}
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