Argument parsing warning

[brendanofallon]

Hi, I recently tried running convading 1.1.6 with a few new command line arguments, and got an unexpected warning. Specifically, when I enter something like:

CoNVaDING.pl -mode StartWithBestScore \
 -inputDir match_controls \
 -outputDir final_calls.z2c  \
 -zScoreCutOffLow -2 \
 -zScoreCutOffHigh 2 \
 -controlsDir convading_controls

I get the following warning:

Unknown option: 2

Is convading trying to somehow parse the value for zScoreCutoffHigh as a new argument? I'm a bit worried that it's not understanding / ignoring my arguments. Is there a way to verify that it is working correctly?

[ljohansson]

Please try to put double quotes around the -2. It looks like perl is interpreting the 2 as an option:

CoNVaDING.pl -mode StartWithBestScore \ -inputDir match_controls \ -outputDir final_calls.z2c \ -zScoreCutOffLow "-2" \ -zScoreCutOffHigh 2 \ -controlsDir convading_controls

[brendanofallon]

Sorry for the delayed response, but looks like the issue still persists even with double quotes

$ CoNVaDING.pl -mode StartWithBestScore \
 -inputDir match_controls  \
-outputDir final_calls.nominal.defaults  \
-ratioCutOffLow "0.65"  \ 
-ratioCutOffHigh "1.4" \
-zScoreCutOffLow "-3" \
-zScoreCutOffHigh "3" \
-controlsDir convading_controls

 Unknown option: 3

Is there a way to tell which arguments are actually being used in a run?

[ljohansson]

From version 1.2.0 onwards the used arguments are printed to the screen. It is indeed possible that you get the "Unknown option" warning. However, the output should be responding to your settings correctly. If unsure, you can check your calls in the totallist that shows all ratio's and Z-scores.

[freerkvandijk]

Hi Brendan,

Please replace the spaces between the arguments and values, a commandline like the one below should work with negative values:

CoNVaDING.pl -mode=StartWithBestScore \
 -inputDir=match_controls  \
-outputDir=final_calls.nominal.defaults  \
-ratioCutOffLow=0.65  \ 
-ratioCutOffHigh=1.4 \
-zScoreCutOffLow=-3 \
-zScoreCutOffHigh=3 \
-controlsDir=convading_controls