atks/vt — pull request #1 by pkrusche (2014-02-13 11:08:46+00:00)
Title: 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=
##reference=hg19
##contig=
##FORMAT=
##INFO=
##INFO=
#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.