Running example 2 reports usage so we need to update flag - which flag is wrong?

[gregorgorjanc]

Here is what I get when I use the pip-installed AlphaPeel - we should throw an error message saying that there is an unsupported/undefined flag and then we print the usage string - printing just usage string is not that informative (we must highlight first that there is an error)

❯ AlphaPeel -genotypes data/genotypes.txt \
          -pedigree data/pedigree.txt \
          -out outputs/multilocus_with_phase \
          -nCycles 5 \
          -runType multi \
          -maxthreads 6 \
          -geno_threshold 0.98 \
          -hap_threshold 0.98 \
          -geno \
          -hap
usage: AlphaPeel [-h] -out OUT [-runtype RUNTYPE] [-bfile [BFILE ...]] [-genotypes [GENOTYPES ...]] [-phasefile [PHASEFILE ...]]
                 [-seqfile [SEQFILE ...]] [-pedigree [PEDIGREE ...]] [-startsnp STARTSNP] [-stopsnp STOPSNP] [-no_dosages] [-no_seg]
                 [-no_params] [-haps] [-calling_threshold [CALLING_THRESHOLD ...]] [-binary_call_files] [-call_phase]
                 [-writekey WRITEKEY] [-onlykeyed] [-iothreads IOTHREADS] [-maxthreads MAXTHREADS] [-ncycles NCYCLES] [-length LENGTH]
                 [-error ERROR] [-seqerror SEQERROR] [-esterrors] [-estmaf] [-nophasefounders] [-sexchrom] [-mapfile MAPFILE]
                 [-segmapfile SEGMAPFILE] [-segfile SEGFILE]
...

[gregorgorjanc]

Looking at this a bit further, it seems that

          -geno_threshold 0.98 \
          -hap_threshold 0.98 \
          -geno \
          -hap

these 4 flags are not part of the usage string - haven't we updated these when we were renaming/consolidating the flags?

usage: AlphaPeel [-h] -out OUT [-runtype RUNTYPE] [-bfile [BFILE ...]] [-genotypes [GENOTYPES ...]] [-phasefile [PHASEFILE ...]]
                 [-seqfile [SEQFILE ...]] [-pedigree [PEDIGREE ...]] [-startsnp STARTSNP] [-stopsnp STOPSNP] [-no_dosages] [-no_seg]
                 [-no_params] [-haps] [-calling_threshold [CALLING_THRESHOLD ...]] [-binary_call_files] [-call_phase]
                 [-writekey WRITEKEY] [-onlykeyed] [-iothreads IOTHREADS] [-maxthreads MAXTHREADS] [-ncycles NCYCLES] [-length LENGTH]
                 [-error ERROR] [-seqerror SEQERROR] [-esterrors] [-estmaf] [-nophasefounders] [-sexchrom] [-mapfile MAPFILE]
                 [-segmapfile SEGMAPFILE] [-segfile SEGFILE]

[XingerTang]

The example code has not been updated since we migrated from the original flags to the current flags.

[gregorgorjanc]

Please update the example code