bx.intervals.operations package

Submodules

• bx.intervals.operations.base_coverage module
  • base_coverage()
• bx.intervals.operations.complement module
  • complement()
• bx.intervals.operations.concat module
  • concat()
• bx.intervals.operations.coverage module
  • coverage()
• bx.intervals.operations.find_clusters module
  • ClusterNode
    • ClusterNode.getintervals()
    • ClusterNode.getlines()
    • ClusterNode.insert()
    • ClusterNode.push_up()
    • ClusterNode.rotateleft()
    • ClusterNode.rotateright()
  • find_clusters()
• bx.intervals.operations.intersect module
  • intersect()
• bx.intervals.operations.join module
  • findintersect()
  • findoverlap()
  • interval_cmp()
  • join()
• bx.intervals.operations.merge module
  • merge()
• bx.intervals.operations.quicksect module
  • IntervalNode
    • IntervalNode.insert()
    • IntervalNode.intersect()
    • IntervalNode.rotateleft()
    • IntervalNode.rotateright()
    • IntervalNode.traverse()
  • IntervalTree
    • IntervalTree.insert()
    • IntervalTree.intersect()
    • IntervalTree.traverse()
  • bad_sect()
  • main()
  • test_func()
• bx.intervals.operations.subtract module
  • subtract()

Module contents

High level operations on genomic intervals. Most accept and produce iterables of bx.io.inervals.io.GenomicInterval objects.

bx.intervals.operations.bits_clear_in_range(bits, range_start, range_end)

Yield start,end tuples for each span of clear bits in [range_start,range_end)

bx.intervals.operations.bits_set_in_range(bits, range_start, range_end)

Yield start,end tuples for each span of set bits in [range_start,range_end)