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"""
Utilities for VCF files.
"""
def walk_together(*readers):
""" Simultaneously iteratate two or more VCF readers and return
lists of concurrent records from each
reader, with None if no record present. Caller must check the
inputs are sorted in the same way and use the same reference
otherwise behaviour is undefined.
"""
nexts = [reader.next() for reader in readers]
while True:
min_next = min([x for x in nexts if x is not None])
# this line uses equality on Records, which checks the ALTs
# not sure what to do with records that have overlapping but different
# variation
yield [x if x is None or x == min_next else None for x in nexts]
# update nexts that we just yielded
for i, n in enumerate(nexts):
if n is not None and n == min_next:
try:
nexts[i] = readers[i].next()
except StopIteration:
nexts[i] = None
if all([x is None for x in nexts]):
break
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