import sys
import os
import tiddit.DBSCAN as DBSCAN
import numpy
import statistics 
from statistics import mode

def find_discordant_pos(fragment,is_mp):
	if is_mp:
		if fragment[5] == "False" and fragment[8] == "True":
			posA=fragment[3]
			posB=fragment[7]
		elif fragment[5] == "False" and fragment[8] == "False":
			posA=fragment[3]
			posB=fragment[6]
		elif fragment[5] == "True" and fragment[8] == "True":		
			posA=fragment[4]
			posB=fragment[7]
		else:
			posA=fragment[4]
			posB=fragment[6]

	else:
		if fragment[5] == "False" and fragment[8] == "True":
			posA=fragment[4]
			posB=fragment[6]
		elif fragment[5] == "False" and fragment[8] == "False":
			posA=fragment[4]
			posB=fragment[7]
		elif fragment[5] == "True" and fragment[8] == "True":
			posA=fragment[3]
			posB=fragment[6]

		else:
			posA=fragment[3]
			posB=fragment[7]

	return(posA,posB)

def main(prefix,chromosomes,contig_length,samples,is_mp,epsilon,m,max_ins_len,min_contig,skip_assembly):

	discordants={}
	contigs=set([])
	splits={}
	positions={}

	i=0
	for sample in samples:
		for line in open("{}_tiddit/discordants_{}.tab".format(prefix,sample)):
			content=line.rstrip().split("\t")
			chrA=content[1]
			chrB=content[2]
			if contig_length[chrA] < min_contig or contig_length[chrB] < min_contig:
				continue

			if not chrA in positions:
				positions[chrA]={}
			if not chrB in positions[chrA]:
				positions[chrA][chrB]=[]

			if not chrA in discordants:
				discordants[chrA]={}
			if not chrB in discordants[chrA]:
				discordants[chrA][chrB]=[]

			posA,posB=find_discordant_pos(content,is_mp)

			if int(posA) > contig_length[chrA]:
				posA=contig_length[chrA]
				if int(posB) > contig_length[chrB]:
					posA=contig_length[chrB]
	
			discordants[chrA][chrB].append([content[0],sample,"D",posA,content[5],posB,content[8],i,int(content[3]),int(content[4]),int(content[6]),int(content[7])])
			positions[chrA][chrB].append([int(posA),int(posB),i])
			i+=1

		for line in open("{}_tiddit/splits_{}.tab".format(prefix,sample)):
			content=line.rstrip().split("\t")
			chrA=content[1]
			chrB=content[2]
			if contig_length[chrA] < min_contig or contig_length[chrB] < min_contig:
				continue

			if not chrA in positions:
				positions[chrA]={}
			if not chrB in positions[chrA]:
				positions[chrA][chrB]=[]

			if not chrA in discordants:
				discordants[chrA]={}
			if not chrB in discordants[chrA]:
				discordants[chrA][chrB]=[]

			posA=content[3]
			posB=content[5]

			if int(posA) > contig_length[chrA]:
				posA=contig_length[chrA]
			if int(posB) > contig_length[chrB]:
				posB=contig_length[chrB]

			discordants[chrA][chrB].append([content[0],sample,"S",posA,content[4],posB,content[6],i,int(content[7]),int(content[8]),int(content[9]),int(content[10])])
			positions[chrA][chrB].append([int(posA),int(posB),i])
			i+=1

		if not skip_assembly:
			for line in open("{}_tiddit/contigs_{}.tab".format(prefix,sample)):
				content=line.rstrip().split("\t")
				chrA=content[1]
				chrB=content[2]

				if contig_length[chrA] < min_contig or contig_length[chrB] < min_contig:
					continue


				if not chrA in positions:
					positions[chrA]={}
				if not chrB in positions[chrA]:
					positions[chrA][chrB]=[]

				if not chrA in discordants:
					discordants[chrA]={}
				if not chrB in discordants[chrA]:
					discordants[chrA][chrB]=[]


				posA=content[3]
				posB=content[5]

				if int(posA) > contig_length[chrA]:
					posA=contig_length[chrA]
				if int(posB) > contig_length[chrB]:
					posB=contig_length[chrB]

				discordants[chrA][chrB].append([content[0],sample,"A",posA,content[4],posB,content[6],i,int(content[7]),int(content[8]),int(content[9]),int(content[10])])
				positions[chrA][chrB].append([int(posA),int(posB),i])
				contigs.add(i)
				i+=1

	candidates={}
	for chrA in chromosomes:
		if not chrA in positions:
			continue
		if not chrA in candidates:
			candidates[chrA]={}

		for chrB in chromosomes:
			if not chrB in positions[chrA]:
				continue
			if not chrB in candidates[chrA]:
				candidates[chrA][chrB]={}

			positions[chrA][chrB]=numpy.array(sorted(positions[chrA][chrB],key=lambda l:l[0]))
			#print(positions[:,[0,1]])
			
			clusters=DBSCAN.main(positions[chrA][chrB],epsilon,m)
			positions[chrA][chrB]=list(positions[chrA][chrB])
			cluster_pos=[]
			for i in range(0,len(positions[chrA][chrB])):
				cluster_pos.append(list(positions[chrA][chrB][i])+[clusters[i]] )
				#positions[i].append(clusters[i])

			cluster_pos= sorted(cluster_pos,key=lambda l:l[2])
			n_ctg_clusters=0
			for i in range(0,len(cluster_pos)):
				candidate=int(cluster_pos[i][-1])
				if candidate == -1 and not (chrA == chrB and discordants[chrA][chrB][i][2] == "A" and ( int(discordants[chrA][chrB][i][5])- int(discordants[chrA][chrB][i][3]) ) < max_ins_len*2):
					continue
				elif candidate == -1 and discordants[chrA][chrB][i][2] == "A":
					candidate=len(cluster_pos)+n_ctg_clusters
					n_ctg_clusters+=1

				if not candidate in candidates[chrA][chrB]:
					candidates[chrA][chrB][candidate]={}
					candidates[chrA][chrB][candidate]["signal_type"]={}
					candidates[chrA][chrB][candidate]["samples"]=set([])
					candidates[chrA][chrB][candidate]["sample_discordants"]={}
					candidates[chrA][chrB][candidate]["sample_splits"]={}
					candidates[chrA][chrB][candidate]["sample_contigs"]={}


					candidates[chrA][chrB][candidate]["N_discordants"]=0
					candidates[chrA][chrB][candidate]["discordants"]=set([])
					candidates[chrA][chrB][candidate]["N_splits"]=0
					candidates[chrA][chrB][candidate]["splits"]=set([])
					candidates[chrA][chrB][candidate]["N_contigs"]=0
					candidates[chrA][chrB][candidate]["contigs"]=set([])


					candidates[chrA][chrB][candidate]["n_signals"]=0

					candidates[chrA][chrB][candidate]["posA"]=0
					candidates[chrA][chrB][candidate]["positions_A"]={}
					candidates[chrA][chrB][candidate]["positions_A"]["contigs"]=[]
					candidates[chrA][chrB][candidate]["positions_A"]["splits"]=[]
					candidates[chrA][chrB][candidate]["positions_A"]["discordants"]=[]
					candidates[chrA][chrB][candidate]["positions_A"]["orientation_contigs"]=[]
					candidates[chrA][chrB][candidate]["positions_A"]["orientation_splits"]=[]
					candidates[chrA][chrB][candidate]["positions_A"]["orientation_discordants"]=[]
					candidates[chrA][chrB][candidate]["positions_A"]["start"]=[]
					candidates[chrA][chrB][candidate]["positions_A"]["end"]=[]

					candidates[chrA][chrB][candidate]["start_A"]=0
					candidates[chrA][chrB][candidate]["end_A"]=0

					candidates[chrA][chrB][candidate]["posB"]=0
					candidates[chrA][chrB][candidate]["positions_B"]={}
					candidates[chrA][chrB][candidate]["positions_B"]["contigs"]=[]
					candidates[chrA][chrB][candidate]["positions_B"]["splits"]=[]
					candidates[chrA][chrB][candidate]["positions_B"]["discordants"]=[]
					candidates[chrA][chrB][candidate]["positions_B"]["orientation_contigs"]=[]
					candidates[chrA][chrB][candidate]["positions_B"]["orientation_splits"]=[]
					candidates[chrA][chrB][candidate]["positions_B"]["orientation_discordants"]=[]
					candidates[chrA][chrB][candidate]["positions_B"]["start"]=[]
					candidates[chrA][chrB][candidate]["positions_B"]["end"]=[]

					candidates[chrA][chrB][candidate]["start_B"]=0
					candidates[chrA][chrB][candidate]["end_B"]=0

				if not discordants[chrA][chrB][i][1] in candidates[chrA][chrB][candidate]["samples"]:
					candidates[chrA][chrB][candidate]["sample_discordants"][discordants[chrA][chrB][i][1]]=set([])
					candidates[chrA][chrB][candidate]["sample_splits"][discordants[chrA][chrB][i][1]]=set([])
					candidates[chrA][chrB][candidate]["sample_contigs"][discordants[chrA][chrB][i][1]]=set([])

				candidates[chrA][chrB][candidate]["samples"].add(discordants[chrA][chrB][i][1])

				candidates[chrA][chrB][candidate]["positions_A"]["start"].append(discordants[chrA][chrB][i][8])
				candidates[chrA][chrB][candidate]["positions_A"]["end"].append(discordants[chrA][chrB][i][9])

				candidates[chrA][chrB][candidate]["positions_B"]["start"].append(discordants[chrA][chrB][i][10])
				candidates[chrA][chrB][candidate]["positions_B"]["end"].append(discordants[chrA][chrB][i][11])

				if discordants[chrA][chrB][i][2] == "D":
					candidates[chrA][chrB][candidate]["discordants"].add(discordants[chrA][chrB][i][0])
					candidates[chrA][chrB][candidate]["positions_A"]["discordants"].append(int(discordants[chrA][chrB][i][3]))
					candidates[chrA][chrB][candidate]["positions_A"]["orientation_discordants"].append(discordants[chrA][chrB][i][4])

					candidates[chrA][chrB][candidate]["positions_B"]["discordants"].append(int(discordants[chrA][chrB][i][5]))
					candidates[chrA][chrB][candidate]["positions_B"]["orientation_discordants"].append(discordants[chrA][chrB][i][6])
					candidates[chrA][chrB][candidate]["sample_discordants"][discordants[chrA][chrB][i][1]].add(discordants[chrA][chrB][i][0])

				elif discordants[chrA][chrB][i][2] == "S":
					candidates[chrA][chrB][candidate]["splits"].add(discordants[chrA][chrB][i][0])
					candidates[chrA][chrB][candidate]["positions_A"]["splits"].append(int(discordants[chrA][chrB][i][3]))
					candidates[chrA][chrB][candidate]["positions_A"]["orientation_splits"].append(discordants[chrA][chrB][i][4])

					candidates[chrA][chrB][candidate]["positions_B"]["splits"].append(int(discordants[chrA][chrB][i][5]))
					candidates[chrA][chrB][candidate]["positions_B"]["orientation_splits"].append(discordants[chrA][chrB][i][6])
					candidates[chrA][chrB][candidate]["sample_splits"][discordants[chrA][chrB][i][1]].add(discordants[chrA][chrB][i][0])
				else:
					candidates[chrA][chrB][candidate]["contigs"].add(discordants[chrA][chrB][i][0])
					candidates[chrA][chrB][candidate]["positions_A"]["contigs"].append(int(discordants[chrA][chrB][i][3]))
					candidates[chrA][chrB][candidate]["positions_A"]["orientation_contigs"].append(discordants[chrA][chrB][i][4])

					candidates[chrA][chrB][candidate]["positions_B"]["contigs"].append(int(discordants[chrA][chrB][i][5]))
					candidates[chrA][chrB][candidate]["positions_B"]["orientation_contigs"].append(discordants[chrA][chrB][i][6])
					candidates[chrA][chrB][candidate]["sample_contigs"][discordants[chrA][chrB][i][1]].add(discordants[chrA][chrB][i][0])



	for chrA in candidates:
		for chrB in candidates[chrA]:
			for candidate in candidates[chrA][chrB]:
				candidates[chrA][chrB][candidate]["N_discordants"]=len(candidates[chrA][chrB][candidate]["discordants"])
				candidates[chrA][chrB][candidate]["N_splits"]=len(candidates[chrA][chrB][candidate]["splits"])
				candidates[chrA][chrB][candidate]["N_contigs"]=len(candidates[chrA][chrB][candidate]["contigs"])

				if candidates[chrA][chrB][candidate]["N_contigs"]:
					candidates[chrA][chrB][candidate]["posA"]=mode(candidates[chrA][chrB][candidate]["positions_A"]["contigs"])
					candidates[chrA][chrB][candidate]["posB"]=mode(candidates[chrA][chrB][candidate]["positions_B"]["contigs"])
				elif candidates[chrA][chrB][candidate]["N_splits"]:
					candidates[chrA][chrB][candidate]["posA"]=mode(candidates[chrA][chrB][candidate]["positions_A"]["splits"])
					candidates[chrA][chrB][candidate]["posB"]=mode(candidates[chrA][chrB][candidate]["positions_B"]["splits"])


				else:
					reverse_A = candidates[chrA][chrB][candidate]["positions_A"]["orientation_discordants"].count("True")
					forward_A = candidates[chrA][chrB][candidate]["positions_A"]["orientation_discordants"].count("False")

					reverse_B = candidates[chrA][chrB][candidate]["positions_B"]["orientation_discordants"].count("True") 
					forward_B = candidates[chrA][chrB][candidate]["positions_B"]["orientation_discordants"].count("False")

					if ( reverse_A >= 5*forward_A or reverse_A*5 <= forward_A ) and ( reverse_B >= 5*forward_B or reverse_B*5 <= forward_B ):
						A_reverse=False
						if reverse_A > forward_A:
							A_reverse=True

						B_reverse=False
						if reverse_B > forward_B:
							B_reverse=True

						if is_mp:
							if A_reverse and not B_reverse:
								candidates[chrA][chrB][candidate]["posA"]=max(candidates[chrA][chrB][candidate]["positions_A"]["discordants"])
								candidates[chrA][chrB][candidate]["posB"]=min(candidates[chrA][chrB][candidate]["positions_B"]["discordants"])

							elif not A_reverse and B_reverse:
								candidates[chrA][chrB][candidate]["posA"]=min(candidates[chrA][chrB][candidate]["positions_A"]["discordants"])
								candidates[chrA][chrB][candidate]["posB"]=max(candidates[chrA][chrB][candidate]["positions_B"]["discordants"])

							elif A_reverse and B_reverse:
								candidates[chrA][chrB][candidate]["posA"]=max(candidates[chrA][chrB][candidate]["positions_A"]["discordants"])
								candidates[chrA][chrB][candidate]["posB"]=max(candidates[chrA][chrB][candidate]["positions_B"]["discordants"])

							else:
								candidates[chrA][chrB][candidate]["posA"]=min(candidates[chrA][chrB][candidate]["positions_A"]["discordants"])
								candidates[chrA][chrB][candidate]["posB"]=min(candidates[chrA][chrB][candidate]["positions_B"]["discordants"])

						else:
							if not A_reverse and B_reverse:
								candidates[chrA][chrB][candidate]["posA"]=max(candidates[chrA][chrB][candidate]["positions_A"]["discordants"])
								candidates[chrA][chrB][candidate]["posB"]=min(candidates[chrA][chrB][candidate]["positions_B"]["discordants"])

							elif A_reverse and not B_reverse:
								candidates[chrA][chrB][candidate]["posA"]=min(candidates[chrA][chrB][candidate]["positions_A"]["discordants"])
								candidates[chrA][chrB][candidate]["posB"]=max(candidates[chrA][chrB][candidate]["positions_B"]["discordants"])

							elif not A_reverse and not B_reverse:
								candidates[chrA][chrB][candidate]["posA"]=max(candidates[chrA][chrB][candidate]["positions_A"]["discordants"])
								candidates[chrA][chrB][candidate]["posB"]=max(candidates[chrA][chrB][candidate]["positions_B"]["discordants"])

							else:
								candidates[chrA][chrB][candidate]["posA"]=min(candidates[chrA][chrB][candidate]["positions_A"]["discordants"])
								candidates[chrA][chrB][candidate]["posB"]=min(candidates[chrA][chrB][candidate]["positions_B"]["discordants"])

					else:
						candidates[chrA][chrB][candidate]["posA"]=mode(candidates[chrA][chrB][candidate]["positions_A"]["discordants"])
						candidates[chrA][chrB][candidate]["posB"]=mode(candidates[chrA][chrB][candidate]["positions_B"]["discordants"])



					candidates[chrA][chrB][candidate]["posA"]
					candidates[chrA][chrB][candidate]["posB"]

				candidates[chrA][chrB][candidate]["startB"]=min(candidates[chrA][chrB][candidate]["positions_B"]["start"])
				candidates[chrA][chrB][candidate]["endB"]=max(candidates[chrA][chrB][candidate]["positions_B"]["end"])

				candidates[chrA][chrB][candidate]["startA"]=min(candidates[chrA][chrB][candidate]["positions_A"]["start"])
				candidates[chrA][chrB][candidate]["endA"]=max(candidates[chrA][chrB][candidate]["positions_A"]["end"])

	return(candidates)

#chromosomes=["1","2","3","4","5"]
#samples=["SweGen0001"]
#prefix=sys.argv[1]
#hej=main(prefix,chromosomes,samples,False,150,2)
##print(hej["3"]["5"])
#for entry in hej["3"]["5"]:
#	print(hej["3"]["5"][entry])
#
