VCF parsing failing test

See comment in vcf.t for a full description of the bug. Fixing this
will require modifications to TreeTime.

The `read_vcf` function is used in augur commands ancestral, refine,
sequence-traits, translate and tree.

tests/functional/ancestral/cram/vcf.t

@@ -0,0 +1,39 @@
+Setup
+
+  $ source "$TESTDIR"/_setup.sh
+
+  $ export DATA="$TESTDIR/../data/simple-genome"
+
+This ~should~ be the same as the first test in general.t, however
+with VCF input instead of a FASTA MSA.
+The output will not have the full sequence attached to every node,
+but it will have the reference sequence attached.
+
+BUG: The SNPs at nt 33 are encoded in the VCF as:
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample_A	sample_B	sample_C
+1	      33	.	  A	  C,G	.	    .	      .	    GT	    1	        2	        0
+where ALT 1 ("C") is on Sample_A and ALT 2 ("G") is on Sample_B.
+The ALT 2 is not being parsed by Augur (Treetime), which results in
+a changed mutation profile at pos 33:
+.       **FASTA input**               **VCF input**
+.         |---G33C-- sample_A           |---A33C-- sample_A
+.  --A33G-|                      -------|
+.         |--------- sample_B           |--------- sample_B
+.
+Because of this bug, the following test fails.
+
+  $ ${AUGUR} ancestral \
+  >  --tree $DATA/tree.nwk \
+  >  --alignment $DATA/snps.vcf \
+  >  --vcf-reference $DATA/reference.fasta \
+  >  --output-node-data "nt_muts.vcf-input.ref-seq.json" \
+  >  --output-vcf "nt_muts.vcf-input.ref-seq.vcf" \
+  >  --inference marginal > /dev/null
+
+
+  $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" \
+  >   "$DATA/nt_muts.ref-seq.json" \
+  >   "nt_muts.vcf-input.ref-seq.json" \
+  >   --exclude-regex-paths "root\['nodes'\]\['.+'\]\['sequence'\]"
+  {}
+

tests/functional/ancestral/data/simple-genome/snps.vcf

@@ -0,0 +1,15 @@
+##fileformat=VCFv4.3
+##contig=<ID=1,length=50>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample_A	sample_B	sample_C
+1	5	.	T	C	.	.	.	GT	1	1	1
+1	7	.	T	G	.	.	.	GT	1	1	0
+1	14	.	C	T	.	.	.	GT	1	1	0
+1	18	.	C	T	.	.	.	GT	0	0	1
+1	28	.	A	N	.	.	.	GT	0	0	1
+1	29	.	A	N	.	.	.	GT	0	0	1
+1	30	.	A	N	.	.	.	GT	0	0	1
+1	33	.	A	C,G	.	.	.	GT	1	2	0
+1	39	.	C	T	.	.	.	GT	1	0	0
+1	42	.	G	A	.	.	.	GT	0	1	0
+1	43	.	A	T	.	.	.	GT	1	1	0