Argument parsing warning

molgenis / CoNVaDING

Copy Number Variation Detection In Next-generation sequencing Gene panels was designed for small (single-exon) copy number variation (CNV) detection in high coverage next-generation sequencing (NGS) data

GNU Lesser General Public License v3.0

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Argument parsing warning #24

Open brendanofallon opened 7 years ago

brendanofallon commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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