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"""
Determine the number of bases covered by a set of intervals.
"""
from bx.intervals.io import BitsetSafeReaderWrapper
from bx.intervals.operations import MAX_END
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 as 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
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