python setup.py install
./test.sh
# Try it out
./example-intersect.py

>>> snps = IntervalFile("testData/snps.hg18.chr21.bed")
>>> rmsk = IntervalFile("testData/rmsk.hg18.chr21.bed")
>>>
>>> # find snps that overlap with repeat annotations
>>> for a in snps:
>>>     for hit in rmsk.search(a.chrom, a.start, a.end):
>>>        print a.chrom, a.start, a.end, a.name,
>>>        print hit.chrom, hit.start, hit.end, hit.name
chr21 9719803 9719804 rs55981545 chr21 9719768 9721892 ALR/Alpha
chr21 9719863 9719864 rs73327798 chr21 9719768 9721892 ALR/Alpha
chr21 9719950 9719951 rs73327799 chr21 9719768 9721892 ALR/Alpha
chr21 9719972 9719973 rs71245703 chr21 9719768 9721892 ALR/Alpha
chr21 9719980 9719981 rs28971396 chr21 9719768 9721892 ALR/Alpha
...