Variants incorrectly labelled AD;AF in callSomatic mode

[JocelynSP]

Describe the bug
Some variants in cancer cell-line samples are being filtered out with flags AF;AD when AF=1 and adequate depth.
Possibly linked to issue #219 but occurring for somatic variants as well as het germline with somatic LOH.

Examples of inappropriate AD;AF filter outputs. Each example has a Normal sample, a human tumour sample, and a cell-line sample grown from the tumour. These are 2 different cases. These depths, of 41 and 45, are typical of the respective samples, i.e., not particularly low or high read depths. Many other variants were not filtered out.

chr17   7674238 .       C       G       10207.9 AD;AF   AC=2;AN=8;DP=190;MP=113.1;MQ=59;NS=3;PP=87.69;SOMATIC   
GT:GQ:DP:MQ:PS:PQ:HSS:HPC:MAP_HF:HF_CR:AD:AF:FT 
0|0:3076:61:60:7674238:100:0,0:80,80:0.5,0.5:0.44,0.56,0.44,0.56:62,.:1,.:PASS        
0|0|1:3076:88:59:7674238:100:0,0,1:4.1,4.1,84:0.044,0.044,0.91:0.016,0.084,0.016,0.084,0.86,0.95:5,87:0.054,0.946:PASS  
0|0|1:3076:41:58:7674238:100:0,0,1:1.5,1.5,39:0.036,0.036,0.93:0.0044,0.092,0.0044,0.092,0.85,0.98:0,42:0,1:AD;AF

chr13   32340756        .       ATAACT  A       10207.9 AD;AF;AFB       AC=3;AN=6;DP=192;MP=57.14;MQ=59;NS=3;PP=3076.53 
GT:GQ:DP:MQ:PS:PQ:AD:AF:FT
1|0:2236:61:60:32340756:91:35,31:0.53,0.47:PASS 
1|0:2236:86:59:32340756:91:10,84:0.106,0.894:AFB
1|0:2236:45:59:32340756:91:0,45:0,1:AD;AF;AFB

Version and command
Octopus is being called from a nix pipeline with

octopus-caller = octopus-caller.overrideAttrs (
    _: rec {
      version = "git";
      src = fetchFromGitHub {
        owner = "luntergroup";
        repo = "octopus";
        rev = "072a0c807505671ab0532c100c84cf62bfb44230";
        sha256 = "sha256-3PQ+IqWZOZU2lgES2I0q3rIiLzuM6IC+5j+ze8635wA=";
      };

      patches = [./sse.patch];

      MEMORY = "10G";
      PPN = "1";
      WALLTIME = "2:00:00";
    }
  );

with

    "env": {
      "JAVA_TOOL_OPTIONS": "-Xmx27g",
      "MEMORY": "30G",
      "PPN": "24",
      "WALLTIME": "48:00:00",
     "buildCommand": "
#  'ln -s' commands to link relevant paths
      octopus -R ref.fa -I *.bam -o $out \
        --bamout $evidence \
        --threads=$NIX_BUILD_CORES \
        --fast \
        -N $normal \
        --annotations AD AF