Variant.originalLine is never set

[arrogantrobot]

The string member of Variant, originalLine, should be set in Variant::parse(string& line, bool parseSamples) of Variant.cpp:

originalLine = line;

Inserted at line 13 or there-abouts should do the trick.

[zeeev]

@arrogantrobot Very late, but ...

The parser deletes the original VCF line to save space. If you want the original line you have two options.

1. Don't parse samples via: variantFile.parseSamples = false;
2. write the var object to a string stream:

stringstream ss;
var << ss;
string ogLine = ss.str();