Passing individuals=[] to ts.write_vcf gives malformed haploid output

[jeromekelleher]

ts = msprime.sim_ancestry(3, sequence_length=1e2, random_seed=1234)
ts = msprime.sim_mutations(ts, rate=0.01, random_seed=1234)
print(ts.as_vcf())

gives

##fileformat=VCFv4.2
##source=tskit 0.5.2.dev0
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=1,length=100>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  tsk_0   tsk_1   tsk_2
1       2       0       C       T       .       PASS    .       GT      1|0     1|0     1|0
1       15      1       G       T       .       PASS    .       GT      1|0     0|0     0|0
1       19      2       A       T       .       PASS    .       GT      1|0     0|0     0|0
1       29      3       C       A       .       PASS    .       GT      1|0     1|0     1|0
1       35      4       T       C       .       PASS    .       GT      0|0     0|0     0|1
1       37      5       G       C       .       PASS    .       GT      0|1     0|1     0|0
1       56      6       C       G       .       PASS    .       GT      0|1     0|1     0|0
1       61      7       T       G       .       PASS    .       GT      0|0     0|0     1|0
1       71      8       C       G       .       PASS    .       GT      0|1     0|1     0|0
1       81      9       G       C       .       PASS    .       GT      1|0     0|0     0|0

But,

ts = msprime.sim_ancestry(3, sequence_length=1e2, random_seed=1234)
ts = msprime.sim_mutations(ts, rate=0.01, random_seed=1234)
print(ts.as_vcf(individuals=[]))

gives

##fileformat=VCFv4.2
##source=tskit 0.5.2.dev0
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=1,length=100>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  tsk_0   tsk_1   tsk_2tsk_3    tsk_4   tsk_5
1       2       0       C       T       .       PASS    .       GT      1       0       1    01       0
1       15      1       G       T       .       PASS    .       GT      1       0       0    00       0
1       19      2       A       T       .       PASS    .       GT      1       0       0    00       0
1       29      3       C       A       .       PASS    .       GT      1       0       1    01       0
1       35      4       T       C       .       PASS    .       GT      0       0       0    00       1
1       37      5       G       C       .       PASS    .       GT      0       1       0    10       0
1       56      6       C       G       .       PASS    .       GT      0       1       0    10       0
1       61      7       T       G       .       PASS    .       GT      0       0       0    01       0
1       71      8       C       G       .       PASS    .       GT      0       1       0    10       0
1       81      9       G       C       .       PASS    .       GT      1       0       0    00       0

Notes tsk_2 and tsk_3 are joined here without a space.

Ideally we'd probably output a "sites only" VCF here, but we can just throw an error here for now for simplicity.