varlens-variants: add an annotation for membership in capture kit intervals

[timodonnell]

No description provided.

[timodonnell]

Relevant code from a pt189 notebook:

nimblegen_df = pandas.read_table("exome-capture-intervals-lists/SeqCap_EZ_Exome_v3.hg19.interval_list", comment='@', names=["contig", "start", "end", "strand", "comment"])
nimblegen_df

sureselect_df = pandas.read_table("exome-capture-intervals-lists/Human_All_Exon_V5.hg19.interval_list", comment='@', names=["contig", "start", "end", "strand", "comment"])
sureselect_df

def make_dict_intervals(df):
    result = collections.defaultdict(intervaltree.IntervalTree)
    total = 0
    for (contig, start, end) in zip(df["contig"], df["start"], df["end"]):
        total += abs(end - start)
        result[contig].addi(start, end)
    print(total)
    return result

nimblegen_intervals = make_dict_intervals(nimblegen_df)
sureselect_intervals = make_dict_intervals(sureselect_df)