Handle unset ref when creating new records

[msto]

Hi,

I found a small bug in the updated VariantHeader.new_record method. When setting the record's initial attributes, the setters' calls to bcf_sync_end raise an exception because record.ref is None.

I added a quick check in bcf_sync_end to handle this case. I think setting ref_len to 0 prior to the INFO/END deletion shouldn't have any side effects, since a new record shouldn't have any alleles or a set END anyways.

This bug could also be solved by setting ref before setting the remaining attributes in new_record, but I wasn't sure what the desired default would be for ref (or if it would be a good idea to force a default).

[bioinformed]

Thanks for the bug report and PR! Much appreciated!

[msto]

No problem, thanks for merging it in so quickly!

I was actually going to follow up with a related bug. In the ref setter method, if the record doesn't already have an associated list of alleles, its list of alleles is set to contain just the ref allele.

pysam/pysam/libcbcf.pyx

Lines 3136 to 3141 in 27d8452

	if r.d.allele and r.n_allele:
	alleles = [r.d.allele[i] for i in range(r.n_allele)]
	alleles[0] = value
	else:
	alleles = [value]
	self.alleles = alleles

However, the alleles setter method raises an exception if passed a list of fewer than 2 alleles.

pysam/pysam/libcbcf.pyx

Lines 3169 to 3170 in 27d8452

	if len(values) < 2:
	raise ValueError('must set at least 2 alleles')

How do you think this one should be solved? Is the allele count restriction necessary? I ran a quick test without it and nothing seemed to break, so I could submit another PR with a quick fix removing that test. If it is necessary, I think setting a new record's ref allele would then require the addition of a dummy or default alternate allele.

[bioinformed]

VCF doesn't allow null alleles and requires at least one alt allele. The easier way to proceed is to require ref and at least one alt to be specified during construction (even if they default to 'N' and '<NON_REF>') and then enforce that requirement globally.