cmpint

Documentation

Overview

The cmpint program compares the intervals in two files. It takes two GTF file inputs describing repeat annotations and compares overlapping regions. The output of the analysis is the number of bases that agree between the inputs, the number of bases that are covered in one, but not the other, and the number of bases where the annotation differs. These analyses are done for both the repeat type and the repeat class, and are emitted on stdout as a JSON object.

If a dot flag is provided, descriptions of the discordances between the feature sets as a graph in DOT format, with edge weights representing counts of mismatched bases.