Order of VariantCollection with sort_key=None

[iskandr]

Issue raised by @tuomastik in a PR:

In the following example, shouldn't a==b and c==d on each loop?

import varcode

variants = [varcode.Variant(contig='1', start=4, ref='', alt=''),
            varcode.Variant(contig='1', start=1, ref='', alt=''),
            varcode.Variant(contig='1', start=3, ref='', alt=''),
            varcode.Variant(contig='1', start=2, ref='', alt='')]

for a, b, c, d in zip(
        varcode.VariantCollection(variants=variants),
        varcode.VariantCollection(variants=variants).variants,
        varcode.VariantCollection(variants=variants, sort_key=None),
        varcode.VariantCollection(variants=variants, sort_key=None).variants):
    print("%s\n%s\n%s\n%s" % (a, b, c, d))
    print("---------------------------------")

Output:

Variant(contig='1', start=1, ref='', alt='', reference_name='GRCh38')
Variant(contig='1', start=4, ref='', alt='', reference_name='GRCh38')
Variant(contig='1', start=1, ref='', alt='', reference_name='GRCh38')
Variant(contig='1', start=4, ref='', alt='', reference_name='GRCh38')
---------------------------------
Variant(contig='1', start=2, ref='', alt='', reference_name='GRCh38')
Variant(contig='1', start=1, ref='', alt='', reference_name='GRCh38')
Variant(contig='1', start=2, ref='', alt='', reference_name='GRCh38')
Variant(contig='1', start=1, ref='', alt='', reference_name='GRCh38')
---------------------------------
Variant(contig='1', start=3, ref='', alt='', reference_name='GRCh38')
Variant(contig='1', start=3, ref='', alt='', reference_name='GRCh38')
Variant(contig='1', start=3, ref='', alt='', reference_name='GRCh38')
Variant(contig='1', start=3, ref='', alt='', reference_name='GRCh38')
---------------------------------
Variant(contig='1', start=4, ref='', alt='', reference_name='GRCh38')
Variant(contig='1', start=2, ref='', alt='', reference_name='GRCh38')
Variant(contig='1', start=4, ref='', alt='', reference_name='GRCh38')
Variant(contig='1', start=2, ref='', alt='', reference_name='GRCh38')

[joaoe]

I had this issue. VariantCollection always sorts. In some cases, I'd want for the order in the input file to be kept. Would also skip some sorting overhead with really big files.