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The genomediff tool only accepts DNA input.
When used with sequence files or encseq, an enhanced suffix array will be
built in memory. The ESA will not be created completely, but construction will
use -memlimit as a threshold and build it partwise, calculating the Shu-length
for each part.
File format for option -unitfile (lua):
units = {
genome1 = { "path/file1.fa", "file2.fa" },
genome2 = { "file3.fa", "path/file4.fa" }
}
Give the path to the files as they were given to the encseq tool!
You can use
gt encseq info INDEXNAME
to get a list of files in an encoded sequence.
Comment lines start with '--' and will be ignored.
See GTDIR/testdata/genomediff/unitfile1.lua for an example.
Options -pl -dc -memlimit are options to influence esa construction.
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