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"""
Merge overlapping regions in two sets of genomic intervals.
"""
from bx.intervals.io import BitsetSafeReaderWrapper
from bx.intervals.operations import (
bits_set_in_range,
MAX_END,
)
# sorting could make this a less memory intensive operation(?)
def merge(interval, mincols=1):
# Handle any ValueError, IndexError and OverflowError exceptions that may be thrown when
# the bitsets are being created by skipping the problem lines
interval = BitsetSafeReaderWrapper(interval, lens={})
bitsets = interval.binned_bitsets()
if interval.header:
yield interval.header
for chrom in bitsets:
bitset = bitsets[chrom]
output = ["."] * (max(interval.chrom_col, interval.start_col, interval.end_col) + 1)
output[interval.chrom_col] = chrom
try:
for start, end in bits_set_in_range(bitset, 0, MAX_END):
output[interval.start_col] = str(start)
output[interval.end_col] = str(end)
yield output
except IndexError as e:
try:
# This will work only if interval is a NiceReaderWrapper
interval.skipped += 1
# no reason to stuff an entire bad file into memmory
if interval.skipped < 10:
interval.skipped_lines.append((interval.linenum, interval.current_line, str(e)))
except Exception:
pass
continue
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