Bases kept lowercase when converting from a GFA

[jmonlong]

1. What were you trying to do?

Convert a GFA to a .vg graph

2. What did you want to happen?

Lowercase bases should be converted to upper case otherwise indexes like the XG index will convert them to Ns. Either during GFA conversion or when indexing, these bases should be converted to upper case?

3. What actually happened?

The bases are kept lowercase which impact mapping later because of their representation as Ns in the xg index.

5. What data and command can the vg dev team use to make the problem happen?

For example for the following GFA:
tiny.gfa.zip

vg convert -g tiny.gfa > convert.tiny.vg
vg view convert.tiny.vg

vg view -F tiny.gfa -v > view.tiny.vg
vg view view.tiny.vg

## both return
# H       VN:Z:1.0
# S       1       GAGCT
# S       2       Tagctag
# L       1       +       2       +       0M

## indexing then introduces Ns
vg index -x convert.tiny.xg convert.tiny.vg
vg view convert.tiny.xg
# H       VN:Z:1.0
# S       1       GAGCT
# S       2       TNNNNNN
# L       1       +       2       +       0M

6. What does running vg version say?

vg version v1.25.0 "Apice"
Compiled with g++ (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0 on Linux
Linked against libstd++ 20191114
Built by anovak@octagon