"""
Complement a set of intervals.
"""

from bx.bitset import MAX
from bx.intervals.io import (
    BitsetSafeReaderWrapper,
    GenomicInterval,
)
from bx.intervals.operations import bits_set_in_range


def complement(reader, lens):
    # Handle any ValueError, IndexError and OverflowError exceptions that may be thrown when
    # the bitsets are being created by skipping the problem lines
    complement_reader = BitsetSafeReaderWrapper(reader, lens=lens)
    bitsets = complement_reader.binned_bitsets(upstream_pad=0, downstream_pad=0, lens=lens)
    # NOT them all
    for key, value in bitsets.items():
        value.invert()
    # Read remaining intervals and subtract
    for chrom in bitsets:
        bitset = bitsets[chrom]
        out_intervals = bits_set_in_range(bitset, 0, lens.get(chrom, MAX))
        try:
            # Write the intervals
            for start, end in out_intervals:
                fields = [
                    "."
                    for x in range(
                        max(complement_reader.chrom_col, complement_reader.start_col, complement_reader.end_col) + 1
                    )
                ]
                # default the column to a + if it exists
                if complement_reader.strand_col < len(fields) and complement_reader.strand_col >= 0:
                    fields[complement_reader.strand_col] = "+"
                fields[complement_reader.chrom_col] = chrom
                fields[complement_reader.start_col] = start
                fields[complement_reader.end_col] = end
                new_interval = GenomicInterval(
                    complement_reader,
                    fields,
                    complement_reader.chrom_col,
                    complement_reader.start_col,
                    complement_reader.end_col,
                    complement_reader.strand_col,
                    "+",
                )
                yield new_interval
        except IndexError as e:
            complement_reader.skipped += 1
            # no reason to stuff an entire bad file into memmory
            if complement_reader.skipped < 10:
                complement_reader.skipped_lines.append(
                    (complement_reader.linenum, complement_reader.current_line, str(e))
                )
            continue


# def main():
#     # test it all out
#     f1 = fileinput.FileInput("dataset_7.dat")
#     g1 = GenomicIntervalReader(f1)
#     for interval in complement(g1,{"chr":16000000}):
#         print "\t".join(interval)
#
# if __name__ == "__main__":
#     main()