function SNPSurvival() -> (CSV statistics,
                           CSV annotResults,
                           CSV annotFull,
                           Latex kmReport,
                           Latex report){

  function SurvivalAnalysis(CSV markers, float pvalue) ->
                           (CSV   statistics,
                            CSV   geneRank,
                            CSV   fullData,
                            Latex kmReport,
                            Latex report){
  // ----------
  //  SETTINGS
  // ----------
  authors    = "Marko Laakso, Riku Louhimo, Sampsa Hautaniemi"
  studyTitle = "Glioblastoma SNP survival analysis"
  cmdLaTeX   = "pdflatex"
  cmdPS2PDF  = "ps2pdf"
  readSNPs   = "changed" //"once"
  pLimit     = pvalue
  caseSQLWhere = "-- No additional restrictions"
  // --------
  //  INPUTS
  // --------
  nullCalls  = "--,ERR"
  useDels    = false
  naLimit    = 0.1
  studyTitle = "Anduril Case Study: "+studyTitle
  /** Clinical parameters for the case samples */
  clinicalData = INPUT(path="data/snp/patient-metadata-caucas.csv")
  /** Column types for the clinical data */
  clinicalTypes = INPUT(path="csv/SNPclinicalTypes.csv")
  /** Select relevant parameters for the survival analysis */
  survivalParamsTemplate = INPUT(path="sql/SNPsurvivalParams.sql")
  /** This SQL is used to generate marker annotation report. */
  annotSQL = INPUT(path="sql/SNPgeneTable.sql")
  /** Generates a list of genes and the marker counts for them. */
  geneRankQuery = INPUT(path="sql/SNPinterestingGenes.sql")
  /** Hyperlink rules for the marker annotations */
  refsHits = INPUT(path="csv/SNPrefsHits.csv")
  /** Hyperlink rules for the gene rank table */
  refsGeneRank = INPUT(path="csv/SNPrefsGeneRank.csv")
  /** Annotations for survival component. */
  snpAnnotations = INPUT(path="csv/SNPAnnotation.csv")

  // -----------
  //  FUNCTIONS
  // -----------
  function GetGenotypes(IDList markers,
                        IDList sampleNames,
                        float  skipFrq) -> (SNPMatrix genotypes,
                                            CSV naDist) {
    genotypes = SNPHelistinReader(config      = genotypeDB,
                                  markerNames = markers,
                                  sampleNames = sampleNames,
                                  skipUnknown = true)
    freqCheck = AlleleCounter(genotypes,
                              dels    = useDels,
                              skip    = skipFrq,
                              naLimit = naLimit)
    ftMarkers = CSV2IDList(freqCheck.frequencies, columnIn="marker", columnOut="marker")
    gtypes    = SNPHelistinReader(config      = genotypeDB,
                                  markerNames = ftMarkers,
                                  sampleNames = sampleNames,
                                  skipUnknown = true)
    return record( genotypes   = gtypes.genotypes,
                   naDist      = freqCheck.naDist )
  }

  function AnnotateSNPs(CSV    markerTable,
                        string caption) -> (Latex           report,
                                            AnnotationTable genes,
                                            CSV             fullData) {
    snpLoci = RefSNPAnnotator(markerTable, keyColumn="marker")
    snpRel  = ExpandCollapse(relation=snpLoci.annotations, listCols="ensembl_gene_stable_id", expand=true)
    genes   = KorvasieniAnnotator(sourceKeys = snpLoci.annotations,
                                  connection = ensembl,
                                  inputDB    = ".GeneId",
                                  inputType  = "Gene",
                                  keyColumn  = "ensembl_gene_stable_id",
                                  isListKey  = true,
                                  targetDB   = ".GeneName,.GeneDesc,.DNABand,GO,UniProt/SwissProt",
                                  unique     = true,
                                  echoColumns = "refsnp_id",
                                  rename     = "UniProt/SwissProt=protein")
    annotData = TableQuery(table1 = snpRel.relation,
                           table2 = genes.bioAnnotation,
                           table3 = markerTable,
                           query  = annotSQL)
    annotTable = CSV2Latex(tabledata = annotData,
                           refs      = refsHits,
                           columns   = "hit,marker,chr,locus,band,gene,gene description",
                           colFormat = "l@{}lr@{:}lp{1cm}p{1.5cm}p{10.5cm}",
                           listCols  = "band",
                           caption   = caption)
    return record( report   = annotTable.report,
                   genes    = genes.bioAnnotation,
                   fullData = annotData.table )
  }

  // ------------
  //  COMPONENTS
  // ------------
  survivalParamsQuery = SearchReplace(survivalParamsTemplate,
                                      key00 = "REP.cond00", value00 = caseSQLWhere)
  survivalClinical = TableQuery(query       = survivalParamsQuery,
                                columnTypes = clinicalTypes,
                                table1      = clinicalData)

  caseNames = CSV2IDList(survivalClinical, columnOut = "SampleId")

  /** Load and preprocess the genotype calls for the cancer patient samples. */
  caseGenotypes = GetGenotypes(markers, caseNames, skipFrq=0.1, @execute = readSNPs)

  clinicalSelect = SourceCode2Latex(source   = survivalParamsQuery,
                                    language = "SQL",
                                    caption  = "This SQL query has been used to select "+
                                               "clinical parameters for the survival calculations.")

  survival = SNPKaplanMeier(genotypes     = caseGenotypes.genotypes,
                            survival      = survivalClinical,
                            annotations   = snpAnnotations,
                            PLimit        = pLimit,
                            naLimit       = naLimit,
                            minFreq       = 0.10,
                            minCount      = 15,
                            timeOutLimit  = 36,
                            survRatePoint = 0.5,
                            timeCol       = "endTime",
                            timeStartCol  = "startTime",
                            statusCol     = "hasEvent",
                            sampleCol     = "sample",
                            skipMissingGT = true,
                            showCI        = true,
                            nullCalls     = nullCalls)

  /** Biological annotations for the survival affecting genes */
  survSNPAnnot = AnnotateSNPs(survival.statistics,
                              caption = "Gene annotations and the loci of the survival "+
                                      "affecting markers")
  survivalStatistics = TableQuery(survival.statistics, survSNPAnnot.fullData,
                                  query = "SELECT table1.*, table2.\"ensembl\" FROM table1 "+
                                          "LEFT OUTER JOIN table2 ON (table1.\"marker\" = table2.\"marker\") ")

  geneRank = QueryReport(query        = geneRankQuery,
                         table1       = survSNPAnnot.fullData,
                         table2       = survival.statistics,
                         refs         = refsGeneRank,
                         section      = "Gene rank",
                         showQuery    = false,
                         showCols     = "gene,markers,p-value,description",
                         colFormat    = "lcrp{11cm}",
                         tableCaption = "A list of survival affecting genes and the marker counts. "+
                                        "P-value is the lowest value for the corresponding markers.")

  survivalReport = LatexCombiner(survival.report,
                                 clinicalSelect.report,
                                 survSNPAnnot.report,
                                 geneRank.report,
                                 pagebreak = true)
  missingDistC = CSV2Latex(caseGenotypes.naDist,
                           colFormat = "p{3cm}r",
                           caption   = "Distribution of the missing values in case samples")
  propertiesDoc = Properties2Latex(genotypeDB,
                                   section = "SNP database configuration")
  reportBody = LatexCombiner(survivalReport,
                             propertiesDoc,
                             missingDistC)
  reportTemplate = LatexTemplate(abstract = abstract,
                                 authors  = authors,
                                 printTOC = true,
                                 title    = studyTitle)
  summaryReport = LatexPDF(header    = reportTemplate.header,
                           footer    = reportTemplate.footer,
                           document  = reportBody.document,
                           latexExec = cmdLaTeX,
                           useRefs   = false)
  return record( statistics = survivalStatistics,
                 geneRank   = geneRank.data,
                 fullData   = survSNPAnnot.fullData,
                 kmReport   = survival.report,
                 report     = reportBody.document )
  }

markers1  = INPUT(path="/opt/sandbox/snpDb/markers/markers1.lst")
markers2  = INPUT(path="/opt/sandbox/snpDb/markers/markers2.lst")
markers3  = INPUT(path="/opt/sandbox/snpDb/markers/markers3.lst")
markers4  = INPUT(path="/opt/sandbox/snpDb/markers/markers4.lst")
markers5  = INPUT(path="/opt/sandbox/snpDb/markers/markers5.lst")
markers6  = INPUT(path="/opt/sandbox/snpDb/markers/markers6.lst")
markers7  = INPUT(path="/opt/sandbox/snpDb/markers/markers7.lst")
markers8  = INPUT(path="/opt/sandbox/snpDb/markers/markers8.lst")
markers9  = INPUT(path="/opt/sandbox/snpDb/markers/markers9.lst")
markers10 = INPUT(path="/opt/sandbox/snpDb/markers/markers10.lst")

survivalSet1  = SurvivalAnalysis(markers=markers1,  pvalue=0.001)
survivalSet2  = SurvivalAnalysis(markers=markers2,  pvalue=0.001)
survivalSet3  = SurvivalAnalysis(markers=markers3,  pvalue=0.001)
survivalSet4  = SurvivalAnalysis(markers=markers4,  pvalue=0.001)
survivalSet5  = SurvivalAnalysis(markers=markers5,  pvalue=0.001)
survivalSet6  = SurvivalAnalysis(markers=markers6,  pvalue=0.001)
survivalSet7  = SurvivalAnalysis(markers=markers7,  pvalue=0.001)
survivalSet8  = SurvivalAnalysis(markers=markers8,  pvalue=0.001)
survivalSet9  = SurvivalAnalysis(markers=markers9,  pvalue=0.001)
survivalSet10 = SurvivalAnalysis(markers=markers10, pvalue=0.001)

combinedSurvivalpre = CSVListJoin(file1 = survivalSet1.statistics,
                                  file2 = survivalSet2.statistics,
                                  file3 = survivalSet3.statistics,
                                  file4 = survivalSet4.statistics,
                                  file5 = survivalSet5.statistics,
                                  file6 = survivalSet6.statistics,
                                  file7 = survivalSet7.statistics,
                                  fileCol = "")
combinedSurvival = CSVListJoin(file1 = combinedSurvivalpre,
                               file2 = survivalSet8.statistics,
                               file3 = survivalSet9.statistics,
                               file4 = survivalSet10.statistics,
                               fileCol = "")
combinedSurvivalpost = SearchReplace(combinedSurvival,
                                     key00 = "A\\.", value00 = "A-")

/** Fetch rsnumbers based on AffySNP-ids */
finalMarkerSetPre = AffySNPFetch(combinedSurvivalpost, snpdb, columnIn="marker")
finalMarkerSet    = CSV2IDList(finalMarkerSetPre, columnIn="marker")
/** Redo analysis with rsIDs and more strict p-value. */
survivalAll    = SurvivalAnalysis(force markers=finalMarkerSet, pvalue=0.0001)

return record( statistics   = survivalAll.statistics,
               annotResults = survivalAll.geneRank,
               annotFull    = survivalAll.fullData,
               kmReport     = survivalAll.kmReport,
               report       = survivalAll.report )
}