how to generate allele.gene.table based on gmap method

[ghost]

Mang thanks for your tools. I have a question, how to use the gmap to generate the allele.gene.table. I've got the allele.contig.table from the gmap alignment, but I found the allele.gene.table is not same as the allele.ctg,table, so could i use the gmap method to generate the allele.gene.table ？