LogR_BAF_FileName[F] -> prepareInput[F];  

                  /getSampleNames
                 |  -> CNVboolVects,
                 |     exportDistMats,
                 |     intersMat_genes,
                 |     exportIntersMat_genes,
                 |     exportCNVDiffMat,
                 |     clustergram,
                 |     distMatGfx,
                 |     CNVDiffMat,
                 |     countCNVlenghts,
                 |     exportToCircos,
                 |     intersectRegs,
                 |     intersectTBRegs
 sampleSheet[F] <
                  \               /genoTypeCheck
                   @prepareInput <
                                  \                          /makeBed
                                   PennCNV[F]               |                    
                                      -> joinPennCNVout[F] <
                                                            \
                                                            |                               /exportPerRegion
                                                            |                              |  -> @exportToCircos
                                                            |                   reformat2 <
                                                            |                /             \ @countCNVlenghts
                                                            |                |              |   -> exportCNVlenghts,
                                                            |                |              |      exportFigCNVlenghts
                                                             addGeneInfo[F]  |
                                                                -> readFile <
                                                                             \             
                                                                              |              /getGeneNames
                                                                              |             |  -> @intersMat_genes,
                                                                              |             |     @clustergram,
                                                                              |             |     @exportIntersMat_genes,
                                                                              |             |     @CNVDiffMat,
                                                                              |             |     @exportCNVDiffMat
                                                                               manualClean <
                                                                                             \   /@intersectRegs
                                                                                              | |   -> exportToCircos,
                                                                                              | |      exportMergedRegs
                                                                                              .<                      
                                                                                                \
                                                                                                 |                    /exportMergedRegsTB
                                                                                                 |   @intersectTBRegs<
                                                                                                 | /                  \mergeFragments
                                                                                                 | |                   |  -> exportMergedFragments,
                                                                                                 | |                   |     exportFigExtRegs  
                                                                                                 .<
                                                                                                   \            
                                                                                                    |             /exportPerRegion_clean
                                                                                                    |           .<
                                                                                                    |          /  \CompareRegionAndGenes
                                                                                                    |         |     -> exportComRegGen
                                                                                                    reformat <
                                                                                                              \           /@intersMat_genes 
                                                                                                               |         |  -> @exportIntersMat_genes
                                                                                                               addStats <
                                                                                                                         \                 /@exportCNVDiffMat,
                                                                                                                         |                |  @clustergram
                                                                                                                         |   @CNVDiffMat <
                                                                                                                         |  /             \ computeFisher
                                                                                                                         | |               |  -> @clustergram,
                                                                                                                         | |               |     @exportCNVDiffMat 
                                                                                                                         .< 
                                                                                                                           \  /@exportCNVDiffMat
                                                                                                                            .< 
                                                                                                                              \             
                                                                                                                              |                /@intersMat_genes
                                                                                                                              |               | -> @exportIntersMat_genes
                                                                                                                               @CNVboolVects <                 
                                                                                                                                              \ samplesDistMats
                                                                                                                                               |  -> @exportDistMats,
                                                                                                                                               |     @distMatGfx
;