LD Reference parameter use is mixed up

[CristiGuijarro]

The Issue

Whilst trying to run GAMBIT on other (non default) LD reference panels for other populations I noticed that the software kept defaulting to "G1K_EUR_3V5/chr$.vcf.gz". This was because I was trying to pass in the --ldref parameter rather than --ldfile. This incorrect usage is also referenced here: https://xqwen.github.io/ptwas/ - the "Quick Start" use case I was following.

Lines of interest

GAMBIT/src/Main.cpp

Line 18 in 1644b80

cerr << " --ldref [data/chr*.vcf.gz] : LD reference panel (\"*\" as wildcard when split by chr)\n";

• https://github.com/corbinq/GAMBIT/blob/master/src/Main.cpp#L98

• https://github.com/corbinq/GAMBIT/blob/master/src/Main.cpp#L191

TLDR;

• in the line above:
  Should be --ldfile rather than --ldref