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analyze_SNPs_hapmap (1 call, 838.921 sec)
Generated 14-Nov-2016 07:47:08 using cpu time.
function in file /home/user/dev/ymap/scripts_seqModules/scripts_WGseq/analyze_SNPs_hapmap.m
Copy to new window for comparing multiple runs

Parents (calling functions)

Function NameFunction TypeCalls
processing3function1
Lines where the most time was spent

Line NumberCodeCallsTotal Time% TimeTime Plot
40
allelic_ratios_WGseq(main_dir,...
1792.314 s94.4%
36
LOH_hapmap_v4(main_dir,user,ge...
146.607 s5.6%
44
end
10 s0%
43
fprintf('*--- End of ''analyze...
10 s0%
39
hapmap = parent_or_hapmap;
10 s0%
All other lines  0 s0%
Totals  838.921 s100% 
Children (called functions)

Function NameFunction TypeCallsTotal Time% TimeTime Plot
allelic_ratios_WGseqfunction1792.304 s94.4%
LOH_hapmap_v4function146.607 s5.6%
num2strfunction10 s0%
fgetlfunction10 s0%
Self time (built-ins, overhead, etc.)  0.010 s0.0%
Totals  838.921 s100% 
Code Analyzer results
Line numberMessage
12The value assigned to variable 'figureDir' might be unused.
14The value assigned to variable 'INDEL_verString' might be unused.
16The value assigned to variable 'rDNA_verString' might be unused.
19The value assigned to variable 'referenceCHR' might be unused.
29The value assigned to variable 'exampleChrName' might be unused.
Coverage results
Show coverage for parent directory
Total lines in function44
Non-code lines (comments, blank lines)17
Code lines (lines that can run)27
Code lines that did run24
Code lines that did not run3
Coverage (did run/can run)88.89 %
Function listing
time 
calls 
 line
   1 
function [] = analyze_SNPs_hapmap(main_dir, user, genomeUser, project, parent_or_hapmap, genome, ploidyEstimateString,ploidyBaseString)
   2 
% analyze_CNVS(<Project Name>,<Project File>,<Ploidy Estimate)
   3 
% A componant of the sequence analysis pipeline, analyzing SNPs only.
   4 
%    <Project Name>    : the name of the project.
   5 
%    <Project File>    : the name of the project file, including directory location.
   6 
%    <Ploidy Estimate> : a numerical value for ploidy from other work.
   7 

   8 
% log file start, for in-process analysis.
      1 
   9 
fprintf(['project : [[[' project '[[[\n']); 
  10 

      1 
  11 
workingDir             = [main_dir 'users/' user '/projects/' project '/']; 
      1 
  12 
figureDir              = workingDir; 
      1 
  13 
CNV_verString          = 'v1'; 
      1 
  14 
INDEL_verString        = 'v1'; 
      1 
  15 
SNP_verString          = 'v4'; 
      1 
  16 
rDNA_verString         = 'v1'; 
      1 
  17 
LOH_verString          = 'v2'; 
      1 
  18 
displayBREAKS          = true; 
      1 
  19 
referenceCHR           = 1; 
  20 

  21 
%% Grab the first column of the first line of the putative_SNP pileup file.
      1 
  22 
datafile       = [workingDir 'putative_SNPs_' SNP_verString '.txt']; 
      1 
  23 
data           = fopen(datafile); 
      1 
  24 
fprintf(['datafile : ' datafile]); 
      1 
  25 
line           = fgetl(data);           % grab the first line of the putative_CNV datafile. 
  26 
% printing first line only if file is not empty
      1 
  27 
if (~feof(data)) 
      1 
  28 
    fprintf(['\n' datafile '::' num2str(data) '::' line '\n']); 
      1 
  29 
    exampleChrName = sscanf(line, '%s',1);  % grab the first column, ex : 'ChrA_C_glabrata_CBS138'; 
  30 
else
  31 
    fprintf('putative_SNPs file is empty');
  32 
end;
      1 
  33 
fclose(data); 
  34 

  35 

 46.61 
      1 
  36 
LOH_hapmap_v4(main_dir,user,genomeUser,project,parent_or_hapmap,genome,ploidyEstimateString,ploidyBaseString,SNP_verString,LOH_verString,CNV_verString,displayBREAKS); 
  37 

      1 
  38 
parent = parent_or_hapmap; 
      1 
  39 
hapmap = parent_or_hapmap; 
 792.31 
      1 
  40 
allelic_ratios_WGseq(main_dir,user,genomeUser,project,parent,hapmap,genome,ploidyEstimateString,ploidyBaseString,SNP_verString,LOH_verString,CNV_verString,displayBREAKS); 
  41 

  42 

      1 
  43 
fprintf('*--- End of ''analyze_SNPs.m'' was reached. ---*\n'); 
      1 
  44 
end