Upper/lower conversion for left-alignment

Left-alignment seems to not work if there are differences in upper/lower caps between the VCF and the reference. 

Here is an example:

```
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##reference=hg19
##contig=<ID=chr22,length=51304566>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##INFO=<ID=_id,Number=1,Type=String,Description="PG ID">
##INFO=<ID=OLD_VARIANT,Number=1,Type=String,Description="Original chr:pos:ref:alt encoding">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  SAMPLE
chr22   41817310        .       a       aA      .       PASS    _id=41817311;OLD_VARIANT=chr22:41817311:A,AA    GT      1/0
```

The reference sequence is 

```
>chr22:41817306-41817312
CAAAAAT
```

... so the variant should move to 41817306 to be totally left aligned.

Here is a proposal for a fix (assuming that this isn't a desired feature). Other bits of the code may have similar behaviour.