Input: completeGenome.txt and genomeInScaffold.txt.
As in the sample test data here, the format for input files:
- Each line represents a scaffold, and there is at least one space between two successive genes.
- A gene name can be any string without spaces. A default “+”is understood for all the genes on one of the strands, but an explicit “-“ sign must be added to all genes located on the other strand.
- In genomeInScaffold.txt file, we use “gap” to represent a gap into which missing genes can be inserted.
In addition there are implicit gaps at the beginning and end off each scaffold, and “gap” need not, and in fact should not,
be written there.