Check for non-symbolic alt alleles before left aligning in liftover

[kachulis]

During liftover, if the strand switches for an indel, the indel will be left aligned and trimmed. However, in determining whether a variant is an indel to be left aligned, any variant with a multi-character REF allele is marked as an indel and left aligned. The problem is that if all the alt alleles are either symbolic or spanning-deletions, then the left alignment algorithm will left align the variant all the way to the beginning of the contig, where it will set the REF allele to N.

While a variant with a multi-character REF and only symbolic/spanning-del alt seems a bit odd, as far as I can tell it is allowed by the vcf spec, and it can occur fairly naturally in the wild by splitting multiallelics on a vcf which includes spanning deletions. For example

POS   REF        ALT
100    AC         A,*

---> split multiallelics
POS   REF        ALT
100    AC         A
100    AC         *

fixes #1899

[lbergelson]

@kachulis Good find. Looks good to me.