Compare index search performance against bx-python

[csw]

Apples and oranges but should give a rough idea.

[csw]

These don't directly compare well, since bx-python searches one interval at a time while bio-maf can search for a set of intervals.

Single interval search:

• bx-python: 1.780s
• bio-maf (MRI): 2.684s
• bio-maf (JRuby): 4.477s

Multiple interval search:

• bio-maf (MRI): 1.656s
• bio-maf (JRuby, 1 thread): 2.973s
• bio-maf (JRuby, 4 threads): 1.596s

Bottom line: there is definitely a performance cost to using Kyoto Cabinet, which is exacerbated under JRuby. (Not clear whether this is a JRuby->Java issue or a Java->JNI issue, or both.) However, it's not clear that it's big enough to constitute a problem.