Welcome to PCS indel’s documentation!

Contents:

• Introduction
• 1_extractPCS module
  • Pre-requisites
  • Cluster resources
  • Time, Memory & Disk space
  • Genome Browser
  • Function details
  • PcsSingleCheck
  • checkPCSrevQ()
  • checkPCSrevT()
  • checkPCSsize()
  • checkSpecies()
  • computePCScoords()
  • computePos()
  • initializePCSchecks()
  • isCompatible()
  • performPCSchecks()
  • readChains()
  • readDNA()
  • reverseComplement()
• 2_computeWindows module
  • Pre-requisites
  • Cluster resources
  • Time, Memory & Disk space
  • Function details
  • checkInputFiles()
  • computeWindows()
  • consistencyCheck()
  • distribPCS_all()
  • distribPCS_single()
  • isContiguous()
  • isOverlap()
  • mergePCS_all()
  • mergePCS_pairwise()
  • mergePCS_pairwise_check()
  • mergePCS_pairwise_findPos()
  • mergePCS_pairwise_updLst()
  • printPCS()
• 3_setupEvolTimes module
  • Pre-requisites
  • Cluster resources
  • Time, Memory & Disk space
  • Function details
  • checkPCSsizeDistribFiles()
  • computeSetupInfo_winRefSize()
  • getReferenceValues()
  • initParallelInputs()
  • loadObservedValues()
  • processIteration()
  • selectEvolTimes()
• 4_estimateEvolTimes module
  • Pre-requisites
  • Cluster resources
  • Time, Memory & Disk space
  • Function details
  • estimateEvolTimes_winRefSize()
  • getSampleSizeRef()
  • initParallelInputs()
  • printIgnoredWindows()
  • processIteration()
  • readSampleSizeRefs()
  • readSetup()
• 5_sampleEvolTimes module
  • Pre-requisites
  • Cluster resources
  • Time, Memory & Disk space
  • Function details
  • initParallelInputs()
  • initializeOutputs()
  • processIteration()
  • sampleEvolTimes()
  • sample_pcs()
• 6_1_plotFig_PcsDistribComp module
  • Pre-requisites
  • Time, Memory & Disk space
  • Function details
  • findBin()
  • makeFigure2()
  • plotPCSsizeDistribBig()
  • plotTauDistribSampled_sum()
  • prepareDataForPlotting()
• 6_2_plotFig_EvolTimesComp module
  • Pre-requisites
  • Time, Memory & Disk space
  • Function details
  • getDistances()
  • getEmptyWindows()
  • loadData()
  • loadOurData()
  • makeColormap()
  • makeFigure3()
  • meanEvolTimes()
  • parseMapping()
  • plotComparisonEvolTimes()
  • rgba_to_hex()
• 6_4_plotFig_FuncClasses module
  • Pre-requisites
  • Time, Memory & Disk space
  • Function details
  • getAnnotOrder()
  • getAnnotTitles()
  • getColors()
  • get_aspect()
  • groupWindowsByAnnotType()
  • loadAnnotations()
  • loadEvolEstimates()
  • makeAnnotationMatrix()
  • makeFigure5()
  • makeFigureSuppS8()
  • plotFuncClassDistrib()
  • sortAnnotations()