tanghaibao / quota-alignment

Guided synteny alignment between duplicated genomes (within specified quota constraint)
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make_range() function extend param #4

Open tanghaibao opened 14 years ago

tanghaibao commented 14 years ago

http://github.com/tanghaibao/quota-alignment/blob/master/cluster_utils.py#L139

Although quite uncommon - when extend is set to large a negative value - non-overlapping segments, after correcting the boundaries, can become overlapping. This is not intended behavior.

For example, say two segments (10, 20), (30, 40). and set the extend to be -100 (tolerating distance Nmax 100), becomes (-80, 10) and (-60, 30), thus overlapping.

since we correct all the boundaries before other calculations. not sure how to fix this.