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A0c_AccessoryGenome.m rename recipsize -> dictsize #8

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A0c_AccessoryGenome.m rename recipsize -> dictsize #8

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9 changes: 6 additions & 3 deletions 1_Detection/A0c_AccessoryGenome.m
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,11 @@
path = "/home/isabel/Documents/Doktorarbeit_Mai2022/1_kleinesPaper_BigData/Donor2Bs166/";
fileName = "Bmoj_2NCe";
fileSuffix = "_bcf.vcf";

% genome size of the .dict that .vcf was mapped to = number of letters in .fasta file
dictsize = 4215607; % B.sub Bs166
%dictsize = 4027680; % B.spiz W23 WT

recipsize = 4215607;
maxDP = 50; % Everything covered >= maxDP, is not included in the
% accessory genome
minLength = 0; % Only regions longer minLength bps are considered
Expand Down Expand Up @@ -49,7 +52,7 @@
% 2. Find positions with no entry in the bcf - no read mapped, position
% with no cover --> posMissingMask == 1

posRecip = [1 : recipsize];
posRecip = [1 : dictsize];
posMissingMask = ~ismember(posRecip, posAll);

% include 1.: set all pos where DP < 50: posMissingMask == 1
Expand Down Expand Up @@ -82,5 +85,5 @@
save(savePath + saveName + "_allBP.mat","accList")

%
accessoryFraction = sum(totalLengthFilt)/recipsize;
accessoryFraction = sum(totalLengthFilt)/dictsize;
disp("For " + fileName + ", "+ num2str(accessoryFraction*100, "%0.1f")+ " % of the genome is accessory.");