#retrieving the given parameter

ccs=params[0]

tree=params[1]

extantAdjacencies=params[2]

adjacencyProbs=params[3]

alpha=params[4]

i=params[5]

extantAdjacencies_species_adj=params[6]

outputDirectory=params[7]

reconstructedMarkerCount=params[8]

ancientLeaves=params[9]

allSampleReconstructionStatistic={}

dict_SCJ={}

#output text log

outLog="Sample: "+str(i)+"\n"

#start sampling method

outLog+="Enumerate joint labelings...\n"

jointLabels, first = SR2.enumJointLabelings(ccs)

outLog+="Check valid labels...\n"

validLabels, validAtNode = SR2.validLabels(jointLabels, first)

outLog+= "Compute ancestral labels with SR...\n"

reconstructedAdj = SR2.sampleLabelings(tree, ccs, validAtNode, extantAdjacencies, adjacencyProbs, alpha, ancientLeaves)

SR2.outputReconstructedAdjacencies(reconstructedAdj, outputDirectory+"/reconstructed_adjacencies_" + str(i))

for node in reconstructedAdj:

# count for each adjaency on each internal node, how often this adjacencies over all samples occurs there

for adjacency in reconstructedAdj[node]:

if (node,adjacency) in allSampleReconstructionStatistic:

allSampleReconstructionStatistic[(node,adjacency)] += 1

else:

allSampleReconstructionStatistic.update({(node,adjacency):1})

outLog+="Scaffolding...\n"

scaffolds = scaffolding.scaffoldAdjacencies(reconstructedAdj)

undoubled = scaffolding.undoubleScaffolds(scaffolds)

scaffolding.outputUndoubledScaffolds(undoubled, outputDirectory+"/undoubled_scaffolds_" + str(i))

scaffolding.outputScaffolds(scaffolds, outputDirectory+"/doubled_scaffolds_" + str(i))

log=scaffolding.sanityCheckScaffolding(undoubled)

outLog+=log

for node in undoubled:

outLog+= str(node)+'\n'

markerCounter = 0

for scaffold in undoubled[node]:

first = scaffold[0]

last = scaffold[-1]

if not first == last:

markerCounter += len(scaffold)

else:

markerCounter = markerCounter + len(scaffold) - 1

outLog+= str(node) + " number of reconstructed undoubled marker in scaffolds: " + str(markerCounter)+'\n'

# number of reconstructed markerIds given by reconstructedMarkerCount

# singleton scaffolds number / number of not reconstructed marker

notReconstructedMarkerCount = reconstructedMarkerCount - markerCounter

# number of all scaffolds

allScaffoldCount = len(undoubled[node]) + notReconstructedMarkerCount

outLog+= str(node) + " number of singleton scaffolds (not reconstructed marker): " + str(notReconstructedMarkerCount)+'\n'

outLog+= str(node) + " number of scaffolds: " + str(allScaffoldCount)+'\n'

scj = calculate_SCJ(tree, reconstructedAdj, extantAdjacencies_species_adj)

outLog+="Single-Cut-or-Join-Distance: " + str(scj)+'\n'

dict_SCJ.update({'Sample_' + str(i): scj})