root/galaxy-central/eggs/bx_python-0.5.0_dev_f74aec067563-py2.6-macosx-10.6-universal-ucs2.egg/bx/intervals/operations/base_coverage.py

"""
Determine the number of bases covered by a set of intervals.
"""

import psyco_full

import traceback
import fileinput
from warnings import warn

from bx.intervals.io import *
from bx.intervals.operations import *

def base_coverage( reader ):
    # Handle any ValueError, IndexError and OverflowError exceptions that may be thrown when
    # the bitsets are being created by skipping the problem lines
    base_reader = BitsetSafeReaderWrapper( reader, lens={} )
    bitsets = base_reader.binned_bitsets()
    coverage = 0
    for chrom in bitsets:
        try:
            coverage += bitsets[chrom].count_range(0, MAX_END)
        except IndexError, e:
            base_reader.skipped += 1
            # no reason to stuff an entire bad file into memmory
            if base_reader.skipped < 10:
                base_reader.skipped_lines.append( ( base_reader.linenum, base_reader.current_line, str( e ) ) )
            continue
    return coverage