VCF Record format/sample write order

[awgymer]

The SAMPLE information for a VariantRecord is written out in the insertion order of the sample dict of the first sample populated for the record. This can lead to two samples in the same VCF having different orders for their FORMAT column which is somewhat unintuitive, although I am not clear if it's an actual bug or against spec.

Here is an MRE:

from pysam import VariantFile, VariantHeader, VariantRecord


header = VariantHeader()
header.contigs.add('chr1')
header.formats.add("GT", "1", "String", "Genotype")
header.formats.add("DP", "1", "Integer", "Read depth in the tumor BAM")
header.formats.add("AF", "1", "Float", "Estimated allele frequency in the tumor BAM")
header.add_samples(['sample1', 'sample2'])


SAMPLE1 = {"GT": (1,0), "DP": 10, "AF": 0.5}
SAMPLE2 = {"GT": (1,0), "DP": 10, "AF": 0.5}

rec1 = header.new_record(
    contig='chr1',
    id='formats_in_order',
    start=0,
    stop=1,
    alleles=('T', 'A')
)

for k, v in SAMPLE1.items():
    rec1.samples['sample1'][k] = v

for k, v in SAMPLE2.items():
    rec1.samples['sample2'][k] = v

rec2 = header.new_record(
    contig='chr1',
    id='first_sample_not_in_order',
    start=0,
    stop=1,
    alleles=('T', 'A')
)

# Note how we insert the sample values in reverse order
for k, v in list(SAMPLE1.items())[::-1]:
    rec2.samples['sample1'][k] = v

for k, v in SAMPLE2.items():
    rec2.samples['sample2'][k] = v

rec3 = header.new_record(
    contig='chr1',
    id='second_sample_not_in_order',
    start=0,
    stop=1,
    alleles=('T', 'A')
)

for k, v in list(SAMPLE2.items())[::-1]:
    rec3.samples['sample2'][k] = v

for k, v in SAMPLE1.items():
    rec3.samples['sample1'][k] = v


testfile = VariantFile('-', 'w', header=header)
testfile.write(rec1)
testfile.write(rec2)
testfile.write(rec3)
testfile.close()

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=chr1>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth in the tumor BAM">
##FORMAT=<ID=AF,Number=1,Type=Float,Description="Estimated allele frequency in the tumor BAM">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample1	sample2
chr1	1	formats_in_order	T	A	.	.	.	GT:DP:AF	1/0:10:0.5	1/0:10:0.5
chr1	1	first_sample_not_in_order	T	A	.	.	.	GT:AF:DP	1/0:0.5:10	1/0:0.5:10
chr1	1	second_sample_not_in_order	T	A	.	.	.	GT:AF:DP	1/0:0.5:10	1/0:0.5:10