get chr names from bam header

Former-commit-id: d58269a6503e0da83f7a19b0943dfe36b8c4cb16

Author: Rebecca Halperin

src/chr2idx.m

@@ -0,0 +1,55 @@
+function chrTable=chr2idx(inputParam)
+%preprocessTumorOnly - creates data structures for tumor only calling
+%calls parsePileupData.packed.pl to parse samtools output
+%
+% Syntax:  [T, E]=preprocessTumorOnly(inputParam,paramFile)
+%
+% Inputs:
+%   inputParam - data structure with the following fields: regionsFile,
+%       numCPU, outname, blockSize, snpVCFpath, snpVCFname,
+%       workingDirectory, tabixPath, NormalBase
+%   
+% Outputs:
+%   T - table of data by position
+%   E - table of data by exon
+%
+% Other m-files required: none
+% Other requirements: parsePileupData.packed.pl, samtools, htslib
+% Subfunctions: none
+% MAT-files required: none
+%
+% See also: TumorOnlyWrapper
+
+% Author: Rebecca F. Halperin, PhD
+% Translational Genomics Research Institute
+% email: [email protected]
+% Website: https://github.com/tgen
+% Last revision: 3-June-2016
+
+%------------- BEGIN CODE --------------
+
+%[status,out]=system('printenv')
+%profile('-memory','on');
+%profile on;
+
+sexChr=regexprep(inputParam.sexChr,'''','')
+sexChr=regexp(sexChr,',','split')
+if max(cellfun('length',sexChr))==0
+    chrList=cellstr(num2str(inputParam.autosomes','%-d'))
+else
+    chrList=[cellstr(num2str(inputParam.autosomes','%-d')); sexChr'];
+end
+
+[~,out]=system(['samtools view -H `head -n1 ' inputParam.bamList ' ` | grep ^@SQ']);
+ 
+contigs=strtok(extractAfter(strsplit(out,'\n'),'SN:')); 
+
+[lia,locb]=ismember(chrList,contigs);
+
+chrTable=table();
+chrTable.chrName=chrList(lia);
+chrTable.chrIdx=locb(lia);
+
+if sum(~lia)>0
+    message=['warning chr ' strjoin(chrList(~lia),',') ' not found in bam']
+end

src/writeSomTable.m

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+function writeSomTable(Tcell,somPos,cloneId,sampleFrac,somaticDetected,outName)
+
+somTable=Tcell{1}(somPos,{'Chr','Pos'});
+somTable.Ref=int2ntIndels(Tcell{1}.RefComb(somPos));
+somTable.A_allele=int2ntIndels(Tcell{1}.Acomb(somPos));
+somTable.B_allele=int2ntIndels(Tcell{1}.Bcomb(somPos));
+somTable.cloneGroup=cloneId(somPos,1);
+somTable.detectStr=num2str(somaticDetected(somPos,:),'%-d');
+somTable.sampleFrac=sampleFrac(somPos,:);
+for i=1:length(Tcell)
+	somTable.Depth(:,i)=Tcell{i}.ReadDepthPass(somPos);
+    somTable.Bcounts(:,i)=Tcell{i}.BcountsComb(somPos);
+end
+somTable.N=Tcell{1}.NumCopies(somPos);
+somTable.M=Tcell{1}.MinAlCopies(somPos);
+
+
+writetable(somTable,[outName '.somaticPass.txt'],'Delimiter','\t','FileType','text','WriteVariableNames',1);