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Load_dataset_information (2 calls, 0.000 sec)
Generated 14-Nov-2016 07:47:09 using cpu time.
function in file /home/user/dev/ymap/scripts_seqModules/Load_dataset_information.m
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Parents (calling functions)

Function NameFunction TypeCalls
LOH_hapmap_v4function1
allelic_ratios_WGseqfunction1
Lines where the most time was spent
No measurable time spent in this function

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end
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load(dataFile);
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fprintf(['\nLoading Common_ChA...
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dataFile = [projectDir 'Common...
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if (exist([projectDir 'Common_...
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Children (called functions)
No children
Code Analyzer results
Line numberMessage
12Use of brackets [] is unnecessary. Use parentheses to group, if needed.
Coverage results
Show coverage for parent directory
Total lines in function56
Non-code lines (comments, blank lines)46
Code lines (lines that can run)10
Code lines that did run5
Code lines that did not run5
Coverage (did run/can run)50.00 %
Function listing
time 
calls 
 line
   1 
function [segmental_aneuploidy] = Load_dataset_information(projectDir)
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%%=========================================================================
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% Load Common_ChARM.mat file for project : 'segmental_aneuploidy'.
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%--------------------------------------------------------------------------
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if (exist([projectDir 'Common_ChARM.mat'],'file') ~= 0) 
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    dataFile = [projectDir 'Common_ChARM.mat']; 
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    fprintf(['\nLoading Common_ChARM.mat file for "' projectDir '" : ' dataFile '\n']); 
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    load(dataFile); 
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else
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    fprintf(['\nThe Common_ChARM.mat file for "' projectDir '" was not found.\n']);
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    fprintf(['Analyze your dataset with "analyze_ChARM.sh" first.\n']);
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    segmental_aneuploidy = [];
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end;
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% %% ====================================================================
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% % Get segmental aneuploidy data for experiment from "segmental_aneuploidy"
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% % This allows for manual annotation of interesting segments of the genome which
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% % differ in apparent copy number...  this is not currently in use and is planned
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% % to be replaced with an automated analysis function based on the ChARM algorithm.
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% %----------------------------------------------------------------------
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% if (exist(['links_dir/pileup_dir/' projectName '_segments.txt'],'file') ~= 0)
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%     fid = fopen(['links_dir/pileup_dir/' projectName '_segments.txt'],'r');
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%     % skip header line.
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%     discard = fgetl(fid);
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%     clear discard;
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% 
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%     % initialize some variables.
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%     i = 0;
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%     lines_analyzed = 0;
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%     counter = 0;
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%     segmental_aneuploidy = [];
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% 
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%     % procss each line of the file.
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%     while not (feof(fid))
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%         i              = i+1;
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%         line           = fgetl(fid);
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%         lines_analyzed = lines_analyzed+1;
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%         
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%         % take of interest data fields from each line.
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%         segAneu_chr        = sscanf(line, '%s',1);
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%         segAneu_break      = sscanf(line, '%s',2);
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%         for k = 1:length(sscanf(line,'%s',1));
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%             segAneu_break(1) = [];
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%         end;
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%         
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%         % interpret probeID to determine probe chromosome number and location.
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%         segmental_aneuploidy(i).chr     = str2double(segAneu_chr);
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%         segmental_aneuploidy(i).break   = str2double(segAneu_break);
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%     end;
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%     fclose(fid);
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% else
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%     segmental_aneuploidy = [];
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% end;
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end