#!/bin/python
# -*- coding: utf-8 -*-
###############################################
#Dresscode : class : uppercase
#            function : begins with a capital
#            variable : words separated by capital
#            object : words separated by underscore
from functionObjectVCF_creator import *
import re
import os
import sys
import subprocess
import re
import time


#      CheckStrandAndReverseNucleotide(self,nucleo):"""Reverse the alt nucleotide if it is needed""" 
char2char = dict() # for fast reverse complement computations
char2char['A'] = 'T'
char2char['T'] = 'A'
char2char['C'] = 'G'
char2char['G'] = 'C'
char2char['a'] = 't'
char2char['t'] = 'a'
char2char['c'] = 'g'
char2char['g'] = 'c'
def ReverseComplement(nucleotide):
        """Take a sequence or a nucleotide and reverse it"""
        return ''.join(char2char[c] for c in nucleotide)[::-1]

#Class and methods_________________________________________________________________________________________________________
#INDEX_____________________________________________________________________________________________________________
#________________class VARIANT(): corresponds to a discosnp bubble with information common to both paths________________ 
#   ______
#__/      \__
#  \______/
# => Methods
#      FillInformationFromHeader(self,VCFObject):"""Parsing of the DiscoSnp++ header"""
#      CheckContigUnitig(self,unitig,contig):"""Checks if there is an extension in the form of contig or unitig to take into account in the mapping position"""
#      RetrievePolymorphismFromHeader(self):'''Gets from the dicoAllele all the positions, and the nucleotides'''
#      MismatchChecker(self):"""In case of divergent main position (case snp whose two paths are mapped ) to define the reference = > check the number of mismatch
#                               ( If the number of mismatch is the same in both cases it is the lower lexicographical SNP which is selected for reference .
#                                The Boolean allows to know the reference SNP ) """      
#      RetrieveGenotypes(self,nbGeno,VCFObject):"""Gets the genotype, the coverage and the likelihood by sample and print it in the correspondand fields. The genotype is determined by DiscoSnp++ (which considered the upper path as reference). If the “REF” corresponds the upper path, the genotype in the VCF is identical to the genotype in DiscoSnp++, else  it's the opposite ( 1/1 becomes 0/0 and so on)."""     
#      FillVCF(self,VCFfile,nbGeno,table,VCFObject): """Take all necessary input variables to fill the vcf;  Fills the fields of the table which will be printed in the vcf ; return the table"""  
#      WhichPathIsTheRef(self,VCFObject): """Finds which path is identical to the reference genome and defines it as the ref : specific method for each type of variant""" 
#      RetrieveMappingPositionCouple(self): """Defines the mapping position for the couple of variant"""
#      CheckCoupleVariantID(self):"""Test if the couple of paths has the same ID"""

#________________class PATH(): """corresponds to one path"""________________
#      RetrieveSeq(self,seq):"""Getter for sequence"""
#      RetrieveDicoMappingPosition(self):"""Retrieves for each path alignment information in a list ; retrieves a dictionary with all the positions of a path and the number of associated mismatch"""
#      CheckBitwiseFlag(self):"""Checks if the BitwiseFlag contains the tested value such as : read reverse strand, read unmmaped and so on."""
#      CigarcodeChecker(self):"""Checks in the cigarcode of the samfile if there is a shift in the alignment between the path and the reference"""
#      ReferenceChecker(self,shift,posCentraleRef,VCFObject):"""Function which allows to get the MD tag parsing; checks if path nucleotide is identical to the reference nucleotide"""
#      RetrieveCoverage(self):"""Get the coverage by path in the discosnp++ header"""
#      GetTag(self):"""Gets the number of mismatch in the samline"""
#      CheckPosVariantFromRef(self,VCFObject): """Checks if the variant is identical to the reference or not ; defines the nucleotide on the reference"""

#________________class SNP(VARIANT):________________
#       WhichPathIsTheRef(self,VCFObject):""""""

#________________class INDEL(VARIANT):________________
#      RetrievePolymorphismFromHeader(self):""""""
#      WhichPathIsTheRef(self,VCFObject):""""""
#      RetrieveMappingPositionCouple(self):""""""

#________________class SNPSCLOSE(VARIANT):________________
#      RetrieveDicoClose(self,dicoCloseUp,dicoCloseLow):
#      WhichPathIsTheRef(self,VCFObject):
#      FillVCF(self,VCFfile,nbGeno,table,VCFObject):

#________________class VCFFIELD():________________
#      PrintOneLine(self,table,VCF):

def shift_from_cigar_code(cigarcode, pospol):
        # print ("shift",cigarcode,pospol)
        parsingCigarCode=re.findall('(\d+|[A-Za-z])',cigarcode) #ParsingCigarCode=['2', 'S', '3', 'M', '1', 'I', '25', 'M']
        # print (parsingCigarCode)
        shift=0
        pos=0
        i=1
        while i<len(parsingCigarCode): #Goes through the list by twos to get all the letters and to take them into account
                local_cigar_code = parsingCigarCode[i]
                previous_local_cigar_code = parsingCigarCode[i-1]
                if local_cigar_code=="S":
                        shift-=int(previous_local_cigar_code)
                        pos+=int(previous_local_cigar_code)
                elif local_cigar_code=="M":
                        pos+=int(previous_local_cigar_code)
                elif local_cigar_code=="D":
                        shift+=int(previous_local_cigar_code)
                elif local_cigar_code=="I":
                        shift-=int(previous_local_cigar_code)#There is a nucleotide of shift compared to the reference
                        pos+=int(previous_local_cigar_code) #We advance in the query SEQ
                #Hard clipping (clipped sequences NOT present in SEQ)
                elif local_cigar_code=="H":
                        shift-=int(previous_local_cigar_code) # It's the shift in the alignment between the reference and the sequence of the variant 
                        pos+=int(previous_local_cigar_code)
                #Padding (silent deletion from padded reference)
                elif local_cigar_code=="P":
                        shift+=int(previous_local_cigar_code)
                        pos+=int(previous_local_cigar_code)
                elif local_cigar_code=="=":
                        pos+=int(previous_local_cigar_code)
                elif local_cigar_code=="X":
                        pos+=int(previous_local_cigar_code)
                        
                if pos>=pospol:
                        # print("return", str(pospol+shift))
                        return pospol+shift#takes into account the shift to add the after the mapping position and the variant position in the sequence                                
                i+=2

        # print("return", str(pospol+shift))
        return pospol+shift#takes into account the shift to add the after the mapping position and the variant position in the sequence

class VARIANT():
        """Object corresponding to a discosnp++ bubble"""
        def __init__(self,line1,line2):
                self.upper_path = PATH(line1)#line in the file corresponding to the upper path
                self.lower_path = PATH(line2)#line in the file corresponding to the lower path
                self.variantID = "" #ID of discoSnp++
                self.discoName = ""#name of the variant : SNP_higher_path_99
                self.len_unitig_left = ""#length of the unitig left
                self.len_unitig_right = ""#length of the unitig right
                self.contigLeft = ""#length of the contig left
                self.contigRight = ""#length of the contig right
                self.rank = ""#rank calculated by discosnp++
                self.nb_pol = ""# number of polymorphism in the disco path 
                self.dicoGeno = {}#dictionnary with the information of the genotype dicoGeno[listgeno[0]] = [listgeno[1],listlikelihood]
                self.dicoAllele = {}#dictionnary of all the information from the header of discosnp++ : depending on the variant
                self.mappingPositionCouple = 0#mapping position of the bubble after correction
                self.dicoIndex = {}#dictionnary with all the index of every items in discoSnp++ header 

#---------------------------------------------------------------------------------------------------------------------------
##Example :SNP_higher_path_99|P_1:30_A/C|high|nb_pol_1|left_unitig_length_129|right_unitig_length_901|C1_0|C2_30|G1_1/1:744,116,6|G2_0/0:6,95,604|rank_1.00000
#---------------------------------------------------------------------------------------------------------------------------                                           
        def FillInformationFromHeader(self,VCFObject):
                """Parsing of the DiscoSnp++ header. Gets unitig, contig, rank, genotypes"""
                headerVariantUp=self.upper_path.listSam[0]#header of the upper path
                # headerVariantLow= self.lower_path.listSam[0]#header of the lower path
                discoList=headerVariantUp.split('|')#splitting the header of discosnp++ into a list
                self.discoName=discoList[0]#fills the attribut discoName of the variant object
                # print discoList
                self.variantID=self.discoName.split("_")[-1]#Gets the variantID ex:56468
                if self.discoName.startswith("SNP"): VCFObject.variantType="SNP"
                else: VCFObject.variantType="INDEL"
                # VCFObject.variantType=self.discoName.split("_")[0]#fills the VCF object with the variant type
                listgeno=[]#splitted informations by genotype contained in the header of discoSnp++
                #Get dicoAllele P_1:30_A/G => {'P_1': ['30', 'A', 'G']} 

                pos=discoList[self.dicoIndex["P_"]].split(',')
                if VCFObject.variantType=="SNP":#Specific dictionary dicoAllele in case of simple snp
                        for item in pos:
                                listP_=item.split(":")
                                self.dicoAllele[listP_[0]]=[(listP_[1].split("_")[0]),(listP_[1].split("_")[1].split("/")[0]),(listP_[1].split("_")[1].split("/")[1])]#{'P_1': ['30', 'A', 'G']}
                elif VCFObject.variantType=="INDEL":#INDEL case : P_1:30_3_2 => {'P_1': ['30', '3', '2']} specific to the INDEL
                        for item in pos:
                                listP_=item.split(":")
                                self.dicoAllele[listP_[0]]=[(listP_[1].split("_")[0]),(listP_[1].split("_")[1]),(listP_[1].split("_")[2])]#  {'P_1': ['30', '3', '2']}

                
                # for item in pos:
                #         if VCFObject.variantType=="SNP":#Specific dictionary dicoAllele in case of simple snp
                #                 # if ":" in item:
                #                 listP_=item.split(":")
                #                 self.dicoAllele[listP_[0]]=[(listP_[1].split("_")[0]),(listP_[1].split("_")[1].split("/")[0]),(listP_[1].split("_")[1].split("/")[1])]#{'P_1': ['30', 'A', 'G']}
                #         elif VCFObject.variantType=="INDEL":#INDEL case : P_1:30_3_2 => {'P_1': ['30', '3', '2']} specific to the INDEL
                #                 listP_=item.split(":")
                #                 self.dicoAllele[listP_[0]]=[(listP_[1].split("_")[0]),(listP_[1].split("_")[1]),(listP_[1].split("_")[2])]#  {'P_1': ['30', '3', '2']}
                #Get unitig
                if "unitig" in self.dicoIndex and "unitig" in headerVariantUp:
                        self.len_unitig_left=int(discoList[self.dicoIndex["unitig"][0]].split("_")[3])
                        self.len_unitig_right=int(discoList[self.dicoIndex["unitig"][1]].split("_")[3])
                #Get contig
                if "contig" in self.dicoIndex and "contig" in headerVariantUp:
                        self.contigLeft=discoList[self.dicoIndex["contig"][0]].split("_")[3] 
                        self.contigRight=discoList[self.dicoIndex["contig"][1]].split("_")[3] 
                #Get rank
                if "rank" in self.dicoIndex and "rank" in headerVariantUp:
                        self.rank=discoList[self.dicoIndex["rank"]].split('_')[1]
                #Get nb_pol
                self.nb_pol=int(discoList[self.dicoIndex["nb_pol"]].split('_')[2])
                if "G" in self.dicoIndex and "G1" in headerVariantUp:
                        for i in self.dicoIndex["G"]:
                                listgeno=discoList[i].replace("_",":").split(":")
                                if len(listgeno)>2:
                                        self.dicoGeno[listgeno[0]]=[listgeno[1],(listgeno[2].split(','))]
                                else:                                     
                                        self.dicoGeno[listgeno[0]]=[listgeno[1]]  
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------              
        
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
        def CheckContigUnitig(self,unitig,contig):
                """Checks if there is an extension in form of contig or unitig to take into account in the position of the variant on the path (if the prediction is not mapped"""
                if contig:#we keep the length of the contig to add it in the event of unmapped path
                        return(int(contig))#return the contig length
                elif unitig:# if there is not a contig we keep the length of the unitig
                        return(int(unitig))#return the unitig length
                else:
                        return 0                                                                                                                                                                                                        
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------                                                   
        def RetrievePolymorphismFromHeader(self):
                '''Gets from the dicoAllele all the positions, and the nucleotides for each variant '''
                for key,(posD,ntUp,ntLow) in self.dicoAllele.items(): #Goes through the dictionary of parsed header
                        self.upper_path.listPosForward.append(int(posD)+1)
                        self.lower_path.listPosForward.append(int(posD)+1)
                        self.upper_path.listPosReverse.append(len(self.upper_path.seq)-int(posD))
                        self.lower_path.listPosReverse.append(len(self.upper_path.seq)-int(posD))
                        self.upper_path.listNucleotideForward.append(ntUp)
                        self.lower_path.listNucleotideForward.append(ntLow)
                        self.upper_path.listNucleotideReverse.append(ReverseComplement(ntUp))
                        self.lower_path.listNucleotideReverse.append(ReverseComplement(ntLow))
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------                                                    
        def MismatchChecker(self):
                """In case of divergent main position (case snp whose two paths are mapped ) to define the reference = > check the number of mismatch
        ( If the number of mismatch is the same in both cases it is the lower lexicographical SNP which is selected for reference .
        The Boolean allows to know the reference SNP : It fills boolRef ) """
                nmUp=None
                nmLow=None
                #Two paths mapped
                if self.upper_path.mappingPosition>0 and self.lower_path.mappingPosition>0:             #Checks if both paths are mapped 
                        nmUp=int(self.upper_path.dicoMappingPos[self.upper_path.mappingPosition][0])    #Distance with the reference for the snpUp
                        nmLow=int(self.lower_path.dicoMappingPos[self.lower_path.mappingPosition][0])   #Distance with the reference for the snpLow
                        # Pierre 25 06 2021: BUG here in case the two paths are not mapped in the same orientation. 
                        if nmUp<nmLow:                                                                  #Checks if the upper path has a distance with the reference smaller than the lower path
                                self.lower_path.boolRef=False                                           # Defines the boolean to know which path will be defined as reference
                                self.upper_path.boolRef=True 
                                self.lower_path.nucleoRef=self.upper_path.nucleoRef
                                self.mappingPosition=self.upper_path.mappingPosition
                        elif nmUp>nmLow :                                                               #Checks if the lower path has a distance with the reference smaller than the upper path
                                self.lower_path.boolRef=True
                                self.upper_path.boolRef=False
                                self.upper_path.nucleoRef=self.lower_path.nucleoRef
                        elif nmUp==nmLow:                                                               #Checks if both path have the same number of difference
                                if self.discoName.split("_")[0]!="INDEL":                               #In case of simple snp
                                        if  self.upper_path.nucleo<self.lower_path.nucleo:              #Checks the lexicographical order
                                                self.lower_path.boolRef=False
                                                self.upper_path.boolRef=True
                                                self.lower_path.nucleoRef=self.upper_path.nucleoRef
                                                self.mappingPosition=self.upper_path.mappingPosition
                                        elif  self.upper_path.nucleo> self.lower_path.nucleo:           #Checks the lexicographical order
                                                self.lower_path.boolRef=True
                                                self.upper_path.boolRef=False
                                                self.upper_path.nucleoRef=self.lower_path.nucleoRef
                                        else :                                                          #If none of the alleles is lexicographically less : checks the mapping position and keeps the lefmost position
                                                if self.upper_path.mappingPosition<self.lower_path.mappingPosition:
                                                        self.lower_path.boolRef=False
                                                        self.upper_path.boolRef=True
                                                        self.lower_path.nucleoRef=self.upper_path.nucleoRef
                                                else:
                                                        self.lower_path.boolRef=True
                                                        self.upper_path.boolRef=False
                                                        self.upper_path.nucleoRef=self.lower_path.nucleoRef
                                else:                                                                   #In case of indel
                                        if self.upper_path.mappingPosition<self.lower_path.mappingPosition: #Checks the mapping position and keeps the lefmost position
                                                self.lower_path.boolRef=False
                                                self.upper_path.boolRef=True
                                        else:
                                                self.lower_path.boolRef=True
                                                self.upper_path.boolRef=False
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------
        def RetrieveGenotypes(self,nbGeno,VCFObject):
                """Gets the phred quality Q, the genotype, the coverage and the likelihood by sample and prints it in the corresponding fields. The genotype is determined by DiscoSnp++ (which considered the upper path as reference). If the “REF” corresponds the upper path, the genotype in the VCF is identical to the genotype in DiscoSnp++, else  it's the opposite ( 1/1 becomes 0/0 and so on)."""
                j=0
                genotypes=""
                key=None
                current_genotype=None
                likelihood=None
                coverage=None
                listcovUp=self.upper_path.listCoverage
                listcovLow=self.lower_path.listCoverage
                listfqUp=self.upper_path.listFQQuality
                listfqLow=self.lower_path.listFQQuality
                if int(nbGeno)==0:
                        VCFObject.formatField=""
                        VCFObject.genotypes=""
                        return
                else:
                        for i in range(0,nbGeno): #for each genotype
                                coverage=f"{listcovUp[i]},{listcovLow[i]}"#defines allele depth 
                                key=f"G{i+1}" # Creates the dictionary key
                                current_genotype = self.dicoGeno[key]#Gets the genotypes associated to the key
                                likelihood=current_genotype[1]#Gets the likelihood associated to the key
                                if listfqUp!="" and listfqLow!="":
                                        fq_quality=f":{listfqUp[i]},{listfqLow[i]}"
                                else :
                                        fq_quality=""
                                if self.lower_path.boolRef==True: #Checks if the mapped path is the lower (in this case exchange 0/0 to 1/1 and 1/1 to 0/0 ; exchanges the likelihood to have the good one for each genotypes)
                                        if listfqUp!="":
                                                fq_quality=f":{listfqLow[i]},{listfqUp[i]}"
                                        else :
                                                fq_quality=""
                                        coverage=f"{listcovLow[i]},{listcovUp[i]}"#Inverts the coverage
                                        #Inverts the first and the last likelihood
                                        likelihoodStart=likelihood[2]
                                        likelihoodEnd=likelihood[0]
                                        likelihood[0]=likelihoodStart
                                        likelihood[2]=likelihoodEnd
                                        #Inverts the genotype
                                        if current_genotype[0] == "0/0": current_genotype[0] = "1/1" 
                                        elif current_genotype[0] == "1/1": current_genotype[0] = "0/0" 
                                        # if "1/1" in current_genotype[0]:
                                        #         current_genotype[0]=current_genotype[0].replace("1/1","0/0")
                                        # elif "0/0" in current_genotype[0]:
                                        #         current_genotype[0]=current_genotype[0].replace("0/0","1/1")
                                if VCFObject.phased==True: #In case of phasing we change the "/" symbol
                                        current_genotype[0]=current_genotype[0].replace("/","|")
                                if isinstance(likelihood,list):
                                        likelihood=str(','.join(current_genotype[1]))
                                else:
                                        likelihood=str(likelihood)
                                genotypes+=str(current_genotype[0])+":"+str(int(listcovUp[i])+int(listcovLow[i]))+":"+likelihood+":"+str(coverage)+str(fq_quality)

                                if i<nbGeno-1 :
                                        genotypes+="\t" #Adds a \t except if this is the last genotype
                #Write results in VCF object
                        VCFObject.formatField="GT:DP:PL:AD"
                        if listfqUp!="":
                                VCFObject.formatField="GT:DP:PL:AD:HQ"  
                        VCFObject.genotypes=genotypes                                                                                                               
    
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------
                                
        def FillVCF(self,VCFfile,nbGeno,table,VCFObject):
                """Take all necessary input variables to fill the vcf;  Fills the fields of the table which will be printed in the vcf ; return the table"""          
                if VCFObject.chrom=="*":
                        table[0]="."
                else:
                        table[0]=VCFObject.chrom
                table[1]=self.mappingPositionCouple
                table[2]=self.variantID
                table[3]=VCFObject.ref

                table[5]="."
                table[6]=VCFObject.filterField
                table[7]=f"Ty={VCFObject.variantType};Rk={self.rank};UL={self.len_unitig_left};UR={self.len_unitig_right};CL={self.contigLeft};CR={self.contigRight};Genome={VCFObject.nucleoRef};Sd={VCFObject.reverse}"
                if VCFObject.filterField=="MULTIPLE" and VCFObject.XA:
                        table[7]+=f";XA={VCFObject.XA}"
                #TODO: eviter ces replace.
                #TODO global: pourquoi stocker les valeurs quand on peut les simplement afficher ?
                # table[7]=table[7].replace("None",".") # Done during VCFObject.PrintOneLine
                table[7]=table[7].replace("none",".") # todo: verifier que ca peut encore arriver
                table[7]=table[7].replace("=;","=.;") # todo: verifier que ca peut encore arriver
                table[8]=VCFObject.formatField
                table[9]=VCFObject.genotypes
                error=VCFObject.CheckOutputConsistency(table,self)
                if error == 0: 
                        VCFObject.PrintOneLine(table,VCFfile) #Print the line into the VCF
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------
                                
        def WhichPathIsTheRef(self,VCFObject):
                """Finds which path is identical to the reference genome (with boolRef) and defines it as the ref : specific method for each type of variant"""       
                #Checks the exception : different mapping position or both paths identical to the reference 
                if ((self.upper_path.mappingPosition>0 and \
                        self.lower_path.mappingPosition>0) \
                        and self.upper_path.mappingPosition!=self.lower_path.mappingPosition):
                        self.MismatchChecker()
                        return
                if self.upper_path.boolRef==self.lower_path.boolRef:
                        self.MismatchChecker()
                        return 
                
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------
        def RetrieveMappingPositionCouple(self): #Validation SNP second part (specific method for close snps)
                """Defines the mapping position for the couple of variant by checking boolRef"""
                #for INDEL and simple snp
                if self.upper_path.boolRef==True:
                        self.mappingPositionCouple=self.upper_path.mappingPosition+int(self.upper_path.correctedPos[0])+int(self.mappingPositionCouple)-1                       
                else:
                        self.mappingPositionCouple=self.lower_path.mappingPosition+int(self.lower_path.correctedPos[0])+int(self.mappingPositionCouple)-1
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------
        # def CheckStrandAndReverseNucleotideNONOPTIMIZED(self,nucleo):
        #         """Reverse the alt nucleotide if it is needed"""
        #         if self.upper_path.boolRef==True:#Checks if the upper path is the reference
        #                 if self.upper_path.boolReverse==self.lower_path.boolReverse :#if the mapping strand is the same on both path => returns the nucleotide
        #                         return(nucleo)
        #                 if self.upper_path.boolReverse=="1" and self.lower_path.boolReverse==".":
        #                         return (nucleo)
        #                 if self.upper_path.boolReverse!=self.lower_path.boolReverse:#if the mapping strand is different on both path => returns the reverse nuclotide
        #                         return (ReverseComplement(nucleo))
        #         elif self.lower_path.boolRef==True:#Checks if the lower path is the reference
        #                 if self.upper_path.boolReverse==self.lower_path.boolReverse or (self.lower_path.boolReverse==1 and self.upper_path.boolReverse=="."):#if the mapping strand is the same on both path => returns the nucleotide
        #                         return (nucleo)
        #                 if self.lower_path.boolReverse=="1" and self.upper_path.boolReverse==".":
        #                         return (nucleo)
        #                 if self.upper_path.boolReverse!=self.lower_path.boolReverse:#if the mapping strand is different on both path => returns the reverse nucleotide
        #                         return (ReverseComplement(nucleo))
        #         else :
        #                 return (nucleo)
        #
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------
        def CheckStrandAndReverseNucleotide(self,nucleo):
                """Reverse the alt nucleotide if it is needed"""
                if self.upper_path.boolReverse!=self.lower_path.boolReverse:# if the mapping strand is different on both path => returns the reverse nuclotide
                        if (str(self.upper_path.boolReverse)=="1" and self.lower_path.boolReverse==".") or (self.upper_path.boolReverse=="." and str(self.lower_path.boolReverse)=="1"):
                                return nucleo # Case in which one of the two variants matched with a 2 or more indel, thus considered as non mapped. June 3017
                        return ReverseComplement(nucleo)
                else :
                        return nucleo 
#---------------------------------------------------------------------------------------------------------------------------
#Example of supplementary alignment
#INDEL_higher_path_17964|P_1:30_10_8|low|nb_pol_1|left_unitig_length_346|right_unitig_length_815|C1_12|C2_1|G1_0/1:321,17,162|G2_1/1:848,120,10|rank_0.46189	0	gi|224384768|gb|CM000663.1|	191102952	60	52M	*	0	0	AAGAAAAAAGAAATAAAAAAAGAAAAAAAAACGAAATAGCCAGAAGGAATGA	*	NM:i:2	MD:Z:1G9C40	AS:i:45	XS:i:23
#INDEL_lower_path_17964|P_1:30_10_8|low|nb_pol_1|left_unitig_length_346|right_unitig_length_815|C1_20|C2_43|G1_0/1:321,17,162|G2_1/1:848,120,10|rank_0.46189	0	gi|224384768|gb|CM000663.1|	191102966	123S8M1I30M	*	0	0	AAGAAAAAAGAAATAAAAAAAGAAAAAAAAGAAAAAAAAAACGAAATAGCCAGAAGGAATGA	*	NM:i:1	MD:Z:38	AS:i:31	XS:i:29	SA:Z:gi|224384768|gb|CM000663.1|,3668552,-,24S29M1D9M,1,2;
#INDEL_lower_path_17964|P_1:30_10_8|low|nb_pol_1|left_unitig_length_346|right_unitig_length_815|C1_20|C2_43|G1_0/1:321,17,162|G2_1/1:848,120,10|rank_0.46189	2064	gi|224384768|gb|CM000663.1|	3668552	1	24H29M1D9M	*	0	0	TTTTTTTCTTTTTTTTCTTTTTTTATTTCTTTTTTCTT	*	NM:i:2	MD:Z:12C16^T9	AS:i:30	XS:i:26	SA:Z:gi|224384768|gb|CM000663.1|,191102966,+,23S8M1I30M,1,1;	XA:Z:gi|224384768|gb|CM000663.1|,-197957308,27S26M9S,0;
#---------------------------------------------------------------------------------------------------------------------------
        def  CheckCoupleVariantID(self):
                """Test if the couple of paths has the same ID"""                
                IDVariantUp=self.upper_path.listSam[0].split("_")[3]
                IDVariantLow= self.lower_path.listSam[0].split("_")[3]
                bitwiseFlag=int(self.upper_path.listSam[1])                
                if IDVariantUp != IDVariantLow:
                        if bitwiseFlag >0: #& 2048 : #Checks if it's a supplementary alignment
                                print("Supplementary alignment:")
                                print(self.upper_path.listSam)
                                return (2) 
                        else :
                                print("WARNING two consecutive lines do not store the same variant id: ")
                                print(self.upper_path.listSam)
                                print(self.upper_path.listSam[1])
                                print(self.lower_path.listSam)
                                return (2)
                
                else:
                        return (0)                                                                           
#############################################################################################
#############################################################################################
class PATH():
        """corresponds to one path of a discoSnp prediction"""
        def __init__(self,line):
                self.listCoverage=[]                                    #list of all the coverage by sample for the path
                self.dicoMappingPos={}                                  #dictionnary with all the mapping positions associated with their number of mismatches with the reference
                self.listNucleotideReverse=[]                           #list of all the variant (snp) of the path on the reverse strand
                self.listNucleotideForward=[]                           #list of all the variant (snp) of the path on the forward strand                
                self.boolReverse=None                                   #Boolean to know if the strand is reverse(-1) or forward(1)
                self.posMut=None                                        #MD tag of the samfile "MD:Z:5A10A0A25G17" =>  5A10A0A25G17
                self.cigarcode=None                                     #cigarcode of the samfile "61M"
                self.boolRef=None                                       #Boolean to know if the path is identical to the reference
                self.nucleoRef=None                                     #Nucleotide corresponding to the variant on the reference
                self.nucleo=None                                        #nucleotide corresponding of the variant on the path
                self.listPosVariantOnPathToKeep=[]                      #list of the positions of all the variant on the in case of Reverse or Forward mapped path
                self.listPosReverse=[]                                  #mapping position(s) of the variant on the path (if it is mapped on the reverse strand)
                self.listPosForward=[]                                  #mapping position(s) of the variant on the path (if it is mapped on the forward strand)
                self.correctedPos=0                                     #list or position of the mapping variant by taking into account the shift with the reference
                self.listFQQuality=[]                                   #string of all the quality scores of every variant
                if ">" not in line:                                     # Case of samfile
                        self.listSam=line.rstrip('\r').rstrip('\n').split('\t')
                        self.discoName=self.listSam[0]
                        self.seq=self.listSam[9]                        #gets the sequence of the path
                        self.mappingPosition=abs(int(self.listSam[3]))  #mapping position of the path
                        self.RetrieveDicoMappingPosition()
                        self.CheckBitwiseFlag()
                else:                                                   #Mode ghost fastafile
                        line=line.strip('>').split("\n")
                        line.pop()
                        self.listSam=line                                #gets the sequence of the path
                        self.discoName=self.listSam[0]
                        self.seq=""
                        self.mappingPosition=0                           #mapping position of the path 
                        self.boolReverse="."                             #We need to define the absence of strand           

        def RetrieveXA(self,VCFObject):
                localXA=""
                for position,(_,cigarcode) in self.dicoMappingPos.items():
                        if cigarcode!="":
                                chromosome = '_'.join(position.split('_')[:-1])
                                mapping_position = int(position.split('_')[-1])
                                shifted_mapping_position = shift_from_cigar_code(cigarcode,abs(mapping_position)+self.listPosVariantOnPathToKeep[0]-1)
                                localXA+=chromosome+'_'+str(shifted_mapping_position)+","
                
                localXA=localXA.rstrip(',')
                VCFObject.XA = localXA

                
                            
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------                     
        def RetrieveSeq(self,seq):
                """Getter for sequence: fills path object"""
                self.seq=seq        
                
                
        def RetrieveDicoMappingPosition(self):
                """Retrieves for each path alignment information in a list ; retrieves a dictionary with all the positions of a path and the number of associated mismatch"""
                variant=self.listSam
                listXA=None
                strXA=None
                alternative_positions=None
                nbMismatch=None
                variant_position = abs(int(variant[3]))
                variant_chromosome = variant[2]
                #Error list with mapping positions very close to the first position given by bwa
                # listerreur=set([(int(variant[3])-1),(int(variant[3])+1),(int(variant[3])+2),(int(variant[3])+3),(int(variant[3])-3),(int(variant[3])-2),int(variant[3])])
                #Creation of a dict with mapping position associated with number of mismatch
                
                # XA cannot occur in the 11 mandatory fields: QNAME	FLAG	RNAM	POS	MAPQ	CIGAR	RNEXT	PNEXT	TLEN	SEQ	QUAL
                
                if 'XA:Z' in ''.join(variant[11:]): # XA: tag for multiple mapping : Checks if the upper path is multiple mapped : XA Alternative hits; format: (chr,pos,CIGAR,NM;)*
                        for item in variant[11:]: 
                                if "XA:Z" in item:
                                        #Parsing XA tag
                                        listXA=item.split(":")[2].split(';')
                                        strXA = ','.join(listXA)        # TODO: useless (?)
                                        listXA = strXA.split(',')       # TODO: useless (?)
                                        listXA.pop()
                                        alternative_positions=listXA     #position=[chrom1,pos1,cigarcode1,number of mismatch1 , chrom2,pos2,cigarcode2,number of mismatch2,...]. pos_i may be negative, in case of revcomp mapping.
                                        self.XA=item
                                        break                #no need to search for XA in other fields
                        i=1
                        while i<len(alternative_positions): #Runs through the list 4 by 4 to get all the positions 
                                
                                if alternative_positions[i-1]==variant_chromosome and\
                                        abs(int(alternative_positions[i])) > variant_position-4 and\
                                        abs(int(alternative_positions[i])) < variant_position+4: 
                                        i+=4
                                        continue #Checks if the position is not too close to the main one
                                
                                self.dicoMappingPos[alternative_positions[i-1]+"_"+alternative_positions[i]]=[int(alternative_positions[i+2]), alternative_positions[i+1]]#the position is associated to the number of mismatch in a dictionary
                                
                                i+=4
                                

                if variant_position>0:#adds the main mapping position to the dictionary of all mapping positions
                        posMut,nbMismatch=self.GetTag()
                        #In case of mapped variant without MD TAG :
                        self.dicoMappingPos[abs(int(variant[3]))]=[nbMismatch,""]
#---------------------------------------------------------------------------------------------------------------------------
#
#FLAG = field to test
#1   read paired
#2   read mapped in proper pair

#4   read unmapped
#8   mate unmapped
#16   read reverse strand
#32   mate reverse strand
#64   first in pair
#128   second in pair
#256   not primary alignment
#512   read fails platform/vendor quality checks
#1024  read is PCR or optical duplicate
#2048  supplementary alignment
#
#---------------------------------------------------------------------------------------------------------------------------                                                                   
        def CheckBitwiseFlag(self):
                """Checks if the BitwiseFlag contains the tested value such as : read reverse strand, read unmmaped and so on."""
                if int(self.listSam[1]) & 16:#Reverse strand
                        self.boolReverse="-1" 
                        self.listPosVariantOnPathToKeep=self.listPosReverse
                        return
                if int(self.listSam[1]) & 4: #Unmapped
                        self.listPosVariantOnPathToKeep=self.listPosForward
                        self.boolReverse="."  
                        return
                #else:  #Forward strand                   
                self.listPosVariantOnPathToKeep=self.listPosForward
                self.boolReverse="1"        

#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------          
        def CigarcodeChecker(self):
                """Checks in the cigarcode of the samfile if there is a shift in the alignment between the path and the reference"""
                cigarcode=self.listSam[5]               
                parsingCigarCode=re.findall('(\d+|[A-Za-z])',cigarcode) #ParsingCigarCode=['2', 'S', '3', 'M', '1', 'I', '25', 'M']
                listPosRef=[]
                listShift=[]
                somme=0
                shift=0
                pos=0
                i=1
                j=0
                listpol=self.listPosVariantOnPathToKeep
                while i<len(parsingCigarCode):#Goes through the list by twos to get all the letters and to take them into account
                        local_cigar_code = parsingCigarCode[i]
                        previous_local_cigar_code = parsingCigarCode[i-1]
                        if local_cigar_code=="S":
                                shift-=int(previous_local_cigar_code)
                                pos+=int(previous_local_cigar_code)
                        elif local_cigar_code=="M":
                                pos+=int(previous_local_cigar_code)
                        elif local_cigar_code=="D":
                                shift+=int(previous_local_cigar_code)
                        elif local_cigar_code=="I":
                                shift-=int(previous_local_cigar_code)#There is a nucleotide of shift compared to the reference
                                pos+=int(previous_local_cigar_code) #We advance in the query SEQ
                        #Hard clipping (clipped sequences NOT present in SEQ)
                        elif local_cigar_code=="H":
                                shift-=int(previous_local_cigar_code) # It's the shift in the alignment between the reference and the sequence of the variant 
                                pos+=int(previous_local_cigar_code)
                        #Padding (silent deletion from padded reference)
                        elif local_cigar_code=="P":
                                shift+=int(previous_local_cigar_code)
                                pos+=int(previous_local_cigar_code)
                        elif local_cigar_code=="=":
                                pos+=int(previous_local_cigar_code)
                        elif local_cigar_code=="X":
                                pos+=int(previous_local_cigar_code)
                        if len(listpol)==1:#Simple SNP and INDEL
                                if pos>=int(listpol[0]):
                                        posRef=int(listpol[0])+shift#takes into account the shift to add the after the mapping position and the variant position in the sequence                                
                                        listShift.append(shift)
                                        listPosRef.append(posRef)
                                        return(listPosRef,listShift)
                        elif len(listpol)>1:#Close SNPs
                                while int(pos)>=int(listpol[j]):#Goes through the list of position (close snps) and see if the position is affected by the shift (means shift before the position)self.listNucleotideForward
                                        posRef=int(listpol[j])+shift #Add the shift to the position (to get the real position of the snp on the reference)
                                        listPosRef.append(posRef) #Add the position to the list by taking into account the shift only if the current position 
                                        listShift.append(shift)
                                        if j<(len(listpol)-1):
                                                j+=1
                                        else:
                                                return(listPosRef,listShift)
                        i+=2                
#---------------------------------------------------------------------------------------------------------------------------
#Example of unmmaped variant : soft clipping of the variant
#['SNP_higher_path_146392|P_1:30_A/G,P_2:45_C/T,P_3:48_T/G|high|nb_pol_3|left_unitig_length_157|right_unitig_length_564|C1_13|C2_1|G1_0/1:389,20,170|G2_1/1:828,117,10|rank_0.43053', '0', 'gi|224384768|gb|CM000663.1|', '229146041', '52', '79M', '*', '0', '0', 'CTTTCTATCTCAAAAGCAGCCACAGACCACATGTAAACAAATAAGCGGTGCCATGTTCCAATAAAACTTTATTTACAGA', '*', 'NM:i:5', 'MD:Z:15T23G1G4T23G8', 'AS:i:54', 'XS:i:30']
#['SNP_lower_path_146392|P_1:30_A/G,P_2:45_C/T,P_3:48_T/G|high|nb_pol_3|left_unitig_length_157|right_unitig_length_564|C1_24|C2_42|G1_0/1:389,20,170|G2_1/1:828,117,10|rank_0.43053', '16', 'gi|224384768|gb|CM000663.1|', '15779841', '25', '30M49S', '*', '0', '0', 'TCTGTAAATAAAGTTTTATTGGAACATGGCCCCACTTATTTGTTTACACGTGGTCTGTGGCTGCTTTTGAGATAGAAAG', '*', 'NM:i:0', 'MD:Z:30', 'AS:i:30', 'XS:i:25', 'XA:Z:gi|224384768|gb|CM000663.1|,+7370519,52S27M,1;gi|224384768|gb|CM000663.1|,-95561814,27M52S,1;']


#SNP_higher_path_215581|P_1:30_C/G|low|nb_pol_1|left_unitig_length_8|right_unitig_length_1|C1_7|C2_17|G1_0/1:554,48,75|G2_0/1:268,13,248|rank_0.32064	0	gi|224384768|gb|CM000663.1|	232979913	7	31S30M	*	0	0	TCAAGACCAGCCTAGGCAACATAGAGATACCATGTCTCTACAAAAAATTAAAAAAAAAAAA	*	NM:i:0	MD:Z:30	AS:i:30	XS:i:28	XA:Z:gi|224384768|gb|CM000663.1|,-241321283,29M32S,1;gi|224384768|gb|CM000663.1|,-114672467,28M33S,0;
#SNP_lower_path_215581|P_1:30_C/G|low|nb_pol_1|left_unitig_length_8|right_unitig_length_1|C1_31|C2_18|G1_0/1:554,48,75|G2_0/1:268,13,248|rank_0.32064	16	gi|224384768|gb|CM000663.1|	65214684	37	59M2S	*	0	0	TTTTTTTTTTTTAATTTTTTGTAGAGACATCGTATCTCTATGTTGCCTAGGCTGGTCTTGA	*	NM:i:3	MD:Z:16A23A5A12	AS:i:44	XS:i:30
#---------------------------------------------------------------------------------------------------------------------------                               
        def ReferenceChecker(self,shift,posCentraleRef,VCFObject,PosVariant):
                """Function which allows to get the MD tag parsing; checks if path nucleotide is identical to the reference nucleotide"""
                i=0
                posMut,nbMismatch=self.GetTag()
                boolDel=True
                pos=shift
                #Allows or disallows soft clip in BWA
                #if int(shift)<=-(int(PosVariant)):#Test if the variant is really mapped (soft clipping > variant position => unmmaped variant)
                if int(shift)<=-2:#we allow 2 soft clip (for bwa mem)
                        self.boolRef=False
                        self.mappingPosition=0#It is considered that the path is unmapped
                        return()  
                nucleoRef=None
                matchInt=None
                parsingPosMut=re.findall('(\d+|[A-Za-z]|\^)',posMut)
                while i<len(parsingPosMut):#Converts the number into integer 
                        matchInt=re.match(r'\d+',parsingPosMut[i]) #Integer motif
                        if matchInt:
                                parsingPosMut[i]=int(parsingPosMut[i])
                        i+=1
                i=0
                while i<len(parsingPosMut): #Goes through the list to know if the variant is identical to the reference
                        if isinstance(parsingPosMut[i],int): #Checks if it's a number of nucleotide or a letter
                                pos+=parsingPosMut[i] #Adds to pos the current number of the list
                        elif parsingPosMut[i]=="^":#In case of deletion from the reference we have to substract the deletion from the current position  
                                i+=1
                                while boolDel: #Checks if it is still a letter in the deletion to substract it from the current position
                                        if isinstance(parsingPosMut[i],int): #If it is an integer we achieved to take into account the deletion : adds the integer to the current position
                                                boolDel=False
                                                pos+=parsingPosMut[i]
                                        else:
                                                pos-=1 #Substracts the nucleotide from the current position
                                                i+=1
                                boolDel=True
                        else:
                                pos+=1
                        if pos==posCentraleRef: # Checks if the current position pos is identical to the position of the variant 
                                if isinstance(parsingPosMut[i],str): #=> it means that the nucleotide is different in the variant and in the reference
                                        self.boolRef=False
                                        self.nucleoRef=parsingPosMut[i]
                                        break
                                else: #If the last item of the list of the MD tag is an integer => it means that the nucleotide of the allele is identical to the reference
                                        self.boolRef=True
                                        break
                        if pos>posCentraleRef: #If the current position is bigger than the variant position it means that the nucleotide of the variant is identical to the reference
                                self.boolRef=True
                                break
                        i+=1
                if pos<posCentraleRef:#Case of large soft clip
                        self.boolRef=False
                        self.nucleoRef="." 
                VCFObject.nucleoRef=nucleoRef  
# nucleoRef : if the nucleotide is different from the reference return the nucleotide of reference
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------                                         
        def RetrieveCoverage(self,dicoIndex):
                """Gets the coverage by path in the discosnp++ header"""
                if "C" in dicoIndex:
                        spitted_input=self.discoName.split("|")
                        for i in dicoIndex["C"]:
                                # matchC=re.match(r'^C',spitted_input[i])
                                if spitted_input[i][0]=='C':
                                        self.listCoverage.append(spitted_input[i].split('_')[1])

#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------                                         
        def RetrieveQualityFQ(self,dicoIndex):
                """Gets the coverage by path in the discosnp++ header"""
                if "Q" in dicoIndex:
                        spitted_input=self.discoName.split("|")
                        for i in dicoIndex["Q"]:   
                                # matchQ=re.match(r'^Q',self.discoName.split("|")[i])
                                if spitted_input[i][0]=="Q":
                                        self.listFQQuality.append(spitted_input[i].split('_')[1])
                else : self.listFQQuality = ""                              
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------                                             
        def GetTag(self):
                """Gets the number of mismatch in the samline"""
                variant=self.listSam


                #Defines NM tag:
                for field in self.listSam[11:]: # TODO : avoid this loop
                        if "NM:" in field:
                                nbMismatch=int(field.split(":")[-1])#Gets the number of mismatch for the first position given by the mapper       
                                break    
                if abs(int(variant[3]))>0:#Check if the variant is really mapped
                        if "MD:" not in str(variant):#Not MD Tag in the variant we deduce the value from the cigarcode
                                print ("!!! No MD tag in your sam file : Could you try with the last version of bwa (upper than 0.7.8) ?")
                                sys.exit()
                        else:                                              
                                for field in self.listSam[11:]:
                                        if "MD:" in field:
                                                posMut = field.split(":")[2] #MD tag parsing
                                                break
                return (posMut,nbMismatch)               
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------                                             
                        
        def CheckPosVariantFromRef(self,VCFObject): #Validation snp first part
                """Checks if the variant is identical to the reference or not ; defines the nucleotide on the reference"""
                dicoClose={}
                nucleo=None
                boolRef=None
                nucleoRef=None
                if int(self.mappingPosition)>0:
                        #Gets the shift by positions (insertion,deletion,sofclipping) and update of the position on the path
                        listCorrectedPos,listShift=self.CigarcodeChecker()
                        self.correctedPos=listCorrectedPos
                        #Defines if the path is identical to the reference and what is the nucleotide on the reference
                        i=0
                        for i in range(len(listCorrectedPos)):#Loops on the list of corrected positions
                                self.ReferenceChecker(listShift[i],listCorrectedPos[i],VCFObject,self.listPosVariantOnPathToKeep[i])#Checks if the path is identical to the reference genome
                                if int(self.mappingPosition)<=0:# Case => variant considered as unmapped because of soft clipping so we have to check again if the mapping position
                                        break
                                if self.boolReverse=="1" and self.listNucleotideForward!=[]:#If we are on the forward strand => defines the nucleotide for the current snp or indel.
                                        self.nucleo=self.listNucleotideForward[i]
                                        if self.nucleoRef==None:#If there is no reference nucleotide given by ReferenceChecker, it means that the variant is equal to the reference so we defined it !
                                                self.nucleoRef=self.listNucleotideForward[i]
                                elif self.boolReverse=="-1" and self.listNucleotideReverse!=[]:#If we are on the reverse strand => defines the nucleotide for the current snp or indel.
                                        self.nucleo=self.listNucleotideReverse[i]
                                        if self.nucleoRef==None:#If there is no reference nucleotide given by ReferenceChecker, it means that the variant is equal to the reference so we defined it !
                                                self.nucleoRef=self.listNucleotideReverse[i]
                                dicoClose[self.listPosVariantOnPathToKeep[i]]=[(self.boolRef),(self.nucleoRef),(listCorrectedPos[i]),(self.nucleo),(self.boolReverse),(int(listCorrectedPos[i])+int(self.mappingPosition))]#Fills the dictionary to keep all informations for close snps
                                if i==0: #Keeps the information of the first snp/indel to fill the attributs of the path object
                                        boolRef=self.boolRef
                                        nucleoRef=self.nucleoRef
                                        nucleo=self.nucleo
                                self.nucleoRef=None#Resets the reference nucleotide for the next snp (case of close snps)
                                                                                                                                                                                                    
                if int(self.mappingPosition)<=0:#Case of unmapped path
                        listCorrectedPos=self.listPosForward#We keep the forward position for every snps/indel on the path
                        self.listPosVariantOnPathToKeep=self.listPosForward
                        shift=0#There is no shift with the reference
                        self.boolReverse="."
                        self.nucleoRef="."
                        self.boolRef=False
                        boolRef=False
                        nucleoRef='.'
                        self.correctedPos=listCorrectedPos
                        if self.listNucleotideForward!=[]:
                                self.nucleo=self.listNucleotideForward[0]
                                i=0
                                for i in range(len(self.listNucleotideForward)):#Loops on the list of position to fill the dictionary for close snps
                                        dicoClose[self.listPosForward[i]]=[(False),(self.nucleoRef),(listCorrectedPos[i]),(self.listNucleotideForward[i]),self.boolReverse,(int(listCorrectedPos[i])+int(self.mappingPosition))]
                                        if i==0:
                                                boolRef=False
                                                nucleoRef=self.nucleoRef
                                                nucleo=self.nucleo
                
                #Fills the attribut of the path with the information of the first snp/indel        
                self.boolRef=boolRef
                self.nucleoRef=nucleoRef
                self.nucleo=nucleo
                return(dicoClose)                                                                           
#############################################################################################
#############################################################################################
class SNP(VARIANT):
        def __init__(self,line1,line2):
                VARIANT.__init__(self,line1,line2)
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------                     
        def WhichPathIsTheRef(self,VCFObject):
                """Finds which path is identical to the reference genome (with boolRef) and defines it as the ref : specific method for each type of variant"""  
                VARIANT.WhichPathIsTheRef(self,VCFObject)                
                posUnmapped=self.CheckContigUnitig(self.len_unitig_left,self.contigLeft) #Takes into account the lenght of the unitig/contig for the position of unmapped allele (position of the allele on the lower path)
#---------------------------------------------------------------------------------------------------------------------------
##Case : two mapped paths
                if self.upper_path.mappingPosition>0 and self.lower_path.mappingPosition>0:
                        ##The path identical to the reference is the lower path 
                        if self.lower_path.boolRef==True and self.upper_path.boolRef==False:
                                VCFObject.chrom=self.lower_path.listSam[2]
                                VCFObject.ref=self.lower_path.nucleo
                                VCFObject.alt=self.upper_path.nucleo
                                VCFObject.reverse=self.lower_path.boolReverse
                                VCFObject.nucleoRef=self.lower_path.nucleoRef
                        ##The path identical to the reference is the upper path 
                        elif self.upper_path.boolRef==True and self.lower_path.boolRef==False:
                                VCFObject.chrom=self.upper_path.listSam[2]
                                VCFObject.ref=self.upper_path.nucleo
                                VCFObject.alt=self.lower_path.nucleo
                                VCFObject.reverse=self.upper_path.boolReverse
                                VCFObject.nucleoRef=self.upper_path.nucleoRef
                        ##No path is identical to the reference => lexicographique choice
                        elif self.upper_path.boolRef==False and self.lower_path.boolRef==False:
                                if  self.upper_path.nucleo< self.lower_path.nucleo:
                                        VCFObject.chrom=self.upper_path.listSam[2]
                                        VCFObject.ref=self.upper_path.nucleo
                                        VCFObject.alt=self.lower_path.nucleo
                                        VCFObject.reverse=self.upper_path.boolReverse
                                        VCFObject.nucleoRef=self.upper_path.nucleoRef
                                elif  self.upper_path.nucleo> self.lower_path.nucleo:
                                        VCFObject.chrom=self.lower_path.listSam[2]
                                        VCFObject.ref=self.lower_path.nucleo
                                        VCFObject.alt=self.upper_path.nucleo
                                        VCFObject.reverse=self.lower_path.boolReverse
                                        VCFObject.nucleoRef=self.lower_path.nucleoRef

#---------------------------------------------------------------------------------------------------------------------------
##Case : Lower path mapped and upper path unmapped      
                elif self.upper_path.mappingPosition<=0 and self.lower_path.mappingPosition>0:
                        VCFObject.chrom=self.lower_path.listSam[2]
                        VCFObject.ref=self.lower_path.nucleo
                        VCFObject.alt=self.upper_path.nucleo
                        VCFObject.reverse=self.lower_path.boolReverse
                        VCFObject.nucleoRef=self.lower_path.nucleoRef
#---------------------------------------------------------------------------------------------------------------------------
##Case : Upper path mapped and lower path unmapped        
                elif self.upper_path.mappingPosition>0 and self.lower_path.mappingPosition<=0:
                        VCFObject.chrom=self.upper_path.listSam[2]
                        VCFObject.ref=self.upper_path.nucleo
                        VCFObject.alt=self.lower_path.nucleo
                        VCFObject.reverse=self.upper_path.boolReverse
                        VCFObject.nucleoRef=self.upper_path.nucleoRef
#---------------------------------------------------------------------------------------------------------------------------
##Case : Both paths are unmapped       
                elif self.upper_path.mappingPosition<=0 and self.lower_path.mappingPosition<=0:
                        if  self.lower_path.nucleo<self.upper_path.nucleo:
                                VCFObject.chrom=self.lower_path.discoName.split("|")[0]
                                VCFObject.ref=self.lower_path.nucleo
                                VCFObject.alt=self.upper_path.nucleo
                                VCFObject.reverse=self.lower_path.boolReverse
                                VCFObject.nucleoRef=self.lower_path.nucleoRef
                                self.mappingPositionCouple=int(posUnmapped)
                        else:
                                VCFObject.chrom=self.upper_path.discoName.split("|")[0]
                                VCFObject.ref=self.upper_path.nucleo
                                VCFObject.alt=self.lower_path.nucleo
                                VCFObject.reverse=self.upper_path.boolReverse
                                VCFObject.nucleoRef=self.upper_path.nucleoRef
                                self.mappingPositionCouple=int(posUnmapped)
                                
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------                                     
                                
        def FillVCF(self,VCFfile,nbGeno,table,VCFObject):
                table[4]=self.CheckStrandAndReverseNucleotide(str(VCFObject.alt)) 
                VARIANT.FillVCF(self,VCFfile,nbGeno,table,VCFObject)
                                     
#############################################################################################
#############################################################################################
class INDEL(VARIANT):
        def __init__(self,line1,line2):
                VARIANT.__init__(self,line1,line2)
                self.insertForward=None
                self.insertReverse=None
                self.ntStartForward=None
                self.ntStartReverse=None   
                self.smallestSequence=None
                self.longestSequenceForward=None
                self.longestSequenceReverse=None
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------                     
        def RetrievePolymorphismFromHeader(self):
                #Test which is the samllest sequence
                if len(self.upper_path.seq)<len(self.lower_path.seq):
                        self.smallestSequence=self.upper_path.seq
                        if self.lower_path.boolReverse=="1" or self.lower_path.boolReverse==".":
                                self.longestSequenceForward=self.lower_path.seq
                                self.longestSequenceReverse=ReverseComplement(self.lower_path.seq)
                        else:
                                self.longestSequenceForward=ReverseComplement(self.lower_path.seq)
                                self.longestSequenceReverse=self.lower_path.seq
                else:
                        self.smallestSequence=self.lower_path.seq
                        if self.lower_path.boolReverse=="1" or self.lower_path.boolReverse==".":
                                self.longestSequenceForward=self.upper_path.seq
                                self.longestSequenceReverse=ReverseComplement(self.upper_path.seq)
                        else:
                                self.longestSequenceForward=ReverseComplement(self.upper_path.seq)
                                self.longestSequenceReverse=self.upper_path.seq
                for key,(posD,ind,amb) in self.dicoAllele.items():#Goes through the dictionary of parsed header
                        #In case of forward strand mapped
                        #we return the disco indel + the lefmost nucleotide before the indel (by taking into account the ambiguity
                        self.upper_path.listPosForward.append(int(posD)-int(amb))
                        self.lower_path.listPosForward.append(int(posD)-int(amb))
                        self.lower_path.listPosReverse.append(len(self.smallestSequence)-int(posD))
                        self.upper_path.listPosReverse.append(len(self.smallestSequence)-int(posD))
                        
                        self.insertForward=self.longestSequenceForward[(int(posD)-1-int(amb)):(int(posD)-int(amb)+int(ind))]
                        self.insertReverse=self.longestSequenceReverse[len(self.smallestSequence)-int(posD)-1:(len(self.smallestSequence)-int(posD)+int(ind))]
                        self.ntStartForward=self.longestSequenceForward[(int(posD)-1)-int(amb)]#We get the nucleotide just before the insertion by taking into acount the possible ambiguity for the position of the indel
                        self.ntStartReverse=self.longestSequenceReverse[(len(self.smallestSequence)-int(posD)-1)]
                        self.lower_path.nucleo="."
                        self.upper_path.nucleo="."
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------                                                          
        def WhichPathIsTheRef(self,VCFObject):
                #Finds the path identical to the reference
                VARIANT.WhichPathIsTheRef(self,VCFObject)
                posUnmapped=self.CheckContigUnitig(self.len_unitig_left,self.contigLeft) #Takes into account the lenght of the unitig/contig for the position of unmapped allele (position of the allele on the lower path)
                old_boolRef_Up=None
                old_boolRef_Low=None
                #In case of unmapped variant : we have to define a reference
                if self.upper_path.boolRef==False and self.lower_path.boolRef==False: # case of unmapped variant
                        old_boolRef_Up=False
                        old_boolRef_Low=False
                        if self.smallestSequence==self.lower_path.seq:
                                self.upper_path.boolRef=False
                                self.lower_path.boolRef=True
                        else:
                                self.upper_path.boolRef=True
                                self.lower_path.boolRef=False         
                #Checks if the insert corresponds to the upper path or to the lower path and the strand of mapping
                # if the lower path or the upper path is the ref and if it is a reverse mapping : 
                if (self.lower_path.boolRef==True and self.lower_path.boolReverse=="-1") or  (self.upper_path.boolRef==True and self.upper_path.boolReverse=="-1"): 
                        if len(self.lower_path.seq)>len(self.upper_path.seq): #if the sequence of the upper path is the smallest 
                                self.lower_path.nucleo=self.insertReverse
                                self.upper_path.nucleo=self.ntStartReverse
                        else:
                                self.upper_path.nucleo=self.insertReverse
                                self.lower_path.nucleo=self.ntStartReverse 
                #If the upper path or the lower path is the ref and if it is a reference mappind
                # 7/6/2016: CL and PP: changed this elif for the else. Avoids an issue with self.upper_path.nucleo not initialized. Large tests results are the same. 
                else:#if (self.lower_path.boolRef==True and (self.lower_path.boolReverse=="1" or self.lower_path.boolReverse==".")) or (self.upper_path.boolRef==True and (self.upper_path.boolReverse=="1" or self.lower_path.boolReverse==".")):
                        if len(self.lower_path.seq)>len(self.upper_path.seq): #if the sequence of the upper path is the smallest :
                                self.lower_path.nucleo=self.insertForward
                                self.upper_path.nucleo=self.ntStartForward
                        else:
                                self.upper_path.nucleo=self.insertForward
                                self.lower_path.nucleo=self.ntStartForward                                      
                #In case of mapped variant
                if old_boolRef_Low==None and old_boolRef_Up==None: #In case of unmapped variant or too much soft clip we have an other way to fill vcf
                        ##Fills the VCF if the upper path is considered as the reference
                        if self.upper_path.boolRef==True:
                                if len(self.upper_path.nucleo)==len(self.insertForward):
                                        self.upper_path.nucleoRef="."
                                        VCFObject.variantType="DEL"
                                else:
                                        self.upper_path.nucleoRef="."
                                        VCFObject.variantType="INS"
                                if self.upper_path.mappingPosition>0:
                                        VCFObject.chrom=self.upper_path.listSam[2]
                                else:
                                        VCFObject.chrom=self.upper_path.listSam[0].split("|")[0]    
                                VCFObject.ref=self.upper_path.nucleo
                                VCFObject.alt=self.lower_path.nucleo
                                VCFObject.reverse=self.upper_path.boolReverse
                                VCFObject.nucleoRef=self.lower_path.nucleoRef
                        ##Fills the VCF if the lower path is considered as the reference
                        elif self.lower_path.boolRef==True:
                                if len(self.lower_path.nucleo)==len(self.insertForward):
                                        self.lower_path.nucleoRef="."
                                        VCFObject.variantType="DEL"
                                else:
                                        self.lower_path.nucleoRef="."
                                        VCFObject.variantType="INS"
                                if self.lower_path.mappingPosition>0:
                                        VCFObject.chrom=self.lower_path.listSam[2]
                                else:
                                        VCFObject.chrom=self.lower_path.listSam[0].split("|")[0]  
                                VCFObject.ref=self.lower_path.nucleo
                                VCFObject.alt=self.upper_path.nucleo
                                VCFObject.reverse=self.lower_path.boolReverse
                                VCFObject.nucleoRef=self.lower_path.nucleoRef
                # Unmapped variants or too much soft clipped (=> the variant will be considered as unmapped)
                if (self.upper_path.mappingPosition<=0 and self.lower_path.mappingPosition<=0) or (old_boolRef_Low==False and old_boolRef_Up==False):
                        if self.lower_path.boolRef==True:
                                self.mappingPositionCouple=int(posUnmapped)
                        else:
                                self.mappingPositionCouple=int(posUnmapped)
                        if len(self.upper_path.nucleo)==len(self.insertForward):
                                VCFObject.chrom=self.upper_path.discoName.split("|")[0]
                                self.upper_path.boolRef=True
                                self.upper_path.nucleoRef="."
                                VCFObject.variantType="DEL"
                                VCFObject.ref=self.upper_path.nucleo
                                VCFObject.alt=self.lower_path.nucleo
                                VCFObject.reverse=self.upper_path.boolReverse
                                VCFObject.nucleoRef=self.lower_path.nucleoRef
                        else:
                                VCFObject.chrom=self.lower_path.discoName.split("|")[0]
                                self.upper_path.boolRef=False
                                self.upper_path.nucleoRef="."
                                VCFObject.variantType="INS"
                                VCFObject.ref=self.lower_path.nucleo
                                VCFObject.alt=self.upper_path.nucleo
                                VCFObject.reverse=self.lower_path.boolReverse
                                VCFObject.nucleoRef=self.lower_path.nucleoRef
    
        def FillVCF(self,VCFfile,nbGeno,table,VCFObject):
                   table[4]=str(VCFObject.alt) 
                   VARIANT.FillVCF(self,VCFfile,nbGeno,table,VCFObject)                                                                          
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------                          
        def RetrieveMappingPositionCouple(self):
                VARIANT.RetrieveMappingPositionCouple(self)
                self.mappingPositionCouple=int(self.mappingPositionCouple)                                            
#############################################################################################
#############################################################################################
class SNPSCLOSE(VARIANT):
        def __init__(self,line1,line2):
                VARIANT.__init__(self,line1,line2)        
                self.dicoCloseSNPUp={} #dictionnary with all the informations for close snps : boolean to know if the allele is identical to the reference,position on the variant, reverse nucleotide for the allele, if the path is reverse or not, mapping position
                self.dicoCloseSNPLow={}
                
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------                   
        def RetrieveDicoClose(self,dicoCloseUp,dicoCloseLow):# Gets the outputs of the method CheckPosVariantFromRef (PATH CLASS)
                self.dicoCloseSNPUp=dicoCloseUp
                self.dicoCloseSNPLow=dicoCloseLow               
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------                                                                        
                       
        def WhichPathIsTheRef(self,VCFObject):
                VARIANT.WhichPathIsTheRef(self,VCFObject)
                VCFObject.phased=True 
                table = [0] * 10 #Create a 10 cols array
                tablebis=[]
                posUnmapped=self.CheckContigUnitig(self.len_unitig_left,self.contigLeft)
                listPositionPolymorphismeOnPathUp=self.upper_path.listPosVariantOnPathToKeep
                listPositionPolymorphismeOnPathLow=self.lower_path.listPosVariantOnPathToKeep
                VCFObject.nucleoRef=[]
                listPolymorphismPos=[]
##Case : two mapped paths
                if self.upper_path.mappingPosition>0 and self.lower_path.mappingPosition>0:
                        
                        ##Sorts the list of position to get the smallest one and its position in the list unsorted!
                        ##Keeps the close snps to sort them : indeed all the lists and dictionnaries :listnucleoUp,listPositionPolymorphismeOnPathUp,listPositionPolymorphismeOnPathLow,listnucleoLow self.dicoCloseSNPUp,self.dicoCloseSNPLow are classified according to dicoHeader so if we start by sorting we lose the correspondence between data
                        listSortedPosUp=list(listPositionPolymorphismeOnPathUp)
                        listSortedPosUp.sort()
                        indexSmallestPosUp=listPositionPolymorphismeOnPathUp.index(listSortedPosUp[0])
                        listSortedPosLow=list(listPositionPolymorphismeOnPathLow)
                        listSortedPosLow.sort()
                        indexSmallestPosLow=listPositionPolymorphismeOnPathLow.index(listSortedPosLow[0])
                        self.upper_path.boolRef=self.dicoCloseSNPUp[listPositionPolymorphismeOnPathUp[indexSmallestPosUp]][0]
                        self.lower_path.boolRef=self.dicoCloseSNPLow[listPositionPolymorphismeOnPathLow[indexSmallestPosLow]][0]
                        
                        #self.upper_path.boolRef=self.dicoCloseSNPUp[listPositionPolymorphismeOnPathUp[indexSmallestPosUp]][0]
                        #self.lower_path.boolRef=self.dicoCloseSNPLow[listPositionPolymorphismeOnPathLow[indexSmallestPosLow]][0]
                        #Decides what is the smallest position according to the reference path (useful if the paths are not aligned on the same strand)
                        if (self.upper_path.boolRef==False and self.lower_path.boolRef==False) or (self.upper_path.boolRef==True and self.lower_path.boolRef==True):
                                VARIANT.MismatchChecker(self)
                        if self.upper_path.boolRef==True and self.lower_path.boolRef==False: #The smallest position identical to the reference is on the upper path
                                indexSmallestPos=indexSmallestPosUp
                                listPolymorphismPos=listPositionPolymorphismeOnPathUp
                        elif self.lower_path.boolRef==True and self.upper_path.boolRef==False:#The smallest position identical to the reference is on the lower path
                                indexSmallestPos=indexSmallestPosLow
                                listPolymorphismPos=listPositionPolymorphismeOnPathLow
                        elif self.upper_path.boolRef==False and self.lower_path.boolRef==False: #Both paths are different from the reference => choice with the lexicographical order
                                if self.upper_path.nucleo<self.lower_path.nucleo:
                                        indexSmallestPos=indexSmallestPosUp
                                        listPolymorphismPos=listPositionPolymorphismeOnPathUp
                                else:
                                        indexSmallestPos=indexSmallestPosLow
                                        listPolymorphismPos=listPositionPolymorphismeOnPathLow
                        #dicoClose[self.listPosVariantOnPathToKeep[i]]=[self.boolRef,self.nucleoRef,correctedPos[i],nucleo,self.boolReverse,(int(correctedPos[i])+int(self.mappingPosition))]
                        for comptPol in range(len(listPolymorphismPos)): #Goes through the list of the variant position starting with the smallest
                                
                                positionSnpUp=self.dicoCloseSNPUp[listPositionPolymorphismeOnPathUp[comptPol]][5]
                                positionSnpLow=self.dicoCloseSNPLow[listPositionPolymorphismeOnPathLow[comptPol]][5]
                                nucleoUp=self.dicoCloseSNPUp[listPositionPolymorphismeOnPathUp[comptPol]][3]
                                nucleoRefUp=self.dicoCloseSNPUp[listPositionPolymorphismeOnPathUp[comptPol]][1]
                                nucleoLow=self.dicoCloseSNPLow[listPositionPolymorphismeOnPathLow[comptPol]][3]
                                nucleoRefLow=self.dicoCloseSNPLow[listPositionPolymorphismeOnPathLow[comptPol]][1]
                                #Fills the variable table with the vcf fields ; Checks the "REF" path to fill the vcf
                                if self.lower_path.boolRef==True and self.upper_path.boolRef==False: #The lower path is defined as REF
                                
                                        VCFObject.chrom=self.lower_path.listSam[2]
                                        table[1]=int(positionSnpLow)-1
                                        table[3]=nucleoLow
                                        table[4]=self.CheckStrandAndReverseNucleotide(nucleoUp)
                                        VCFObject.nucleoRef.append([nucleoRefLow,positionSnpLow])
                                        VCFObject.reverse=self.lower_path.boolReverse   
                                elif self.upper_path.boolRef==True and self.lower_path.boolRef==False:#The upper path is defined as REF
                                        table[1]=int(positionSnpUp)-1
                                        table[3]=nucleoUp
                                        table[4]=self.CheckStrandAndReverseNucleotide(nucleoLow)
                                        VCFObject.nucleoRef.append([nucleoRefUp,positionSnpUp])
                                        VCFObject.chrom=self.upper_path.listSam[2]
                                        VCFObject.reverse=self.upper_path.boolReverse                             
                                tablebis.append(list(table))#Stocks the variable with all the vcf fields for each close snp to sort it and print it in the vcf
                        tablebis=sorted(tablebis, key=lambda colonnes: colonnes[1])
                        return (tablebis)
#---------------------------------------------------------------------------------------------------------------------------
##Case : Both paths are unmapped     
                elif self.upper_path.mappingPosition <= 0 and self.lower_path.mappingPosition<= 0:
                        self.upper_path.boolReverse="."
                        i=0
                        for i in range(len(listPositionPolymorphismeOnPathUp)):
                                VCFObject.chrom=self.upper_path.discoName.split("|")[0]
                                positionSnpUp=int(listPositionPolymorphismeOnPathUp[i])+int(posUnmapped)
                                positionSnpLow=int(listPositionPolymorphismeOnPathUp[i])+int(posUnmapped)
                                nucleoUp=self.upper_path.listNucleotideForward[i]
                                nucleoRefUp="."
                                nucleoLow=self.lower_path.listNucleotideForward[i]
                                nucleoRefLow="."
                                VCFObject.reverse="."
                                table[1]=positionSnpUp
                                table[3]=nucleoUp
                                table[4]=nucleoLow
                                VCFObject.nucleoRef.append([nucleoRefUp,positionSnpUp])
                                tablebis.append(list(table))
                        tablebis=sorted(tablebis, key=lambda colonnes: colonnes[1])
                        return (tablebis)
#---------------------------------------------------------------------------------------------------------------------------
##Case : Upper path mapped and lower path unmapped  
                elif self.upper_path.mappingPosition>0 and self.lower_path.mappingPosition<=0:
                        comptPol=0
                        VCFObject.chrom=self.upper_path.listSam[2]
                        VCFObject.reverse=self.upper_path.boolReverse
                        for comptPol in range(len(listPositionPolymorphismeOnPathUp)):
                                if (int(self.upper_path.boolReverse)==-1):
                                        nucleoLow=ReverseComplement(self.lower_path.listNucleotideForward[comptPol])
                                        nucleoUp=self.upper_path.listNucleotideReverse[comptPol]
                                elif int(self.upper_path.boolReverse)==1:
                                        nucleoLow=self.lower_path.listNucleotideForward[comptPol]
                                        nucleoUp=self.upper_path.listNucleotideForward[comptPol]
                                nucleoRefLow="."
                                positionSnpUp=int(self.dicoCloseSNPUp[listPositionPolymorphismeOnPathUp[comptPol]][5])-1
                                nucleoRefUp=self.dicoCloseSNPUp[listPositionPolymorphismeOnPathUp[comptPol]][1]
                                table[1]=positionSnpUp
                                table[3]=nucleoUp
                                table[4]=nucleoLow
                                VCFObject.nucleoRef.append([nucleoRefUp,positionSnpUp])
                                tablebis.append(list(table))
                        tablebis=sorted(tablebis, key=lambda colonnes: colonnes[1])
                        return (tablebis)
#---------------------------------------------------------------------------------------------------------------------------
##Case : Lower path mapped and upper path unmapped            
                elif self.upper_path.mappingPosition<=0 and self.lower_path.mappingPosition>0:
                        VCFObject.chrom=self.lower_path.listSam[2]
                        VCFObject.reverse=self.lower_path.boolReverse
                        for comptPol in range(len(listPositionPolymorphismeOnPathLow)):
                                if (int(self.lower_path.boolReverse)==-1):
                                        nucleoUp=ReverseComplement(self.upper_path.listNucleotideForward[comptPol])
                                        nucleoLow=self.lower_path.listNucleotideReverse[comptPol]
                                elif int(self.lower_path.boolReverse)==1:
                                        nucleoUp=self.upper_path.listNucleotideForward[comptPol]
                                        nucleoLow=self.lower_path.listNucleotideForward[comptPol]
                                nucleoRefUp="."
                                positionSnpLow=int(self.dicoCloseSNPLow[listPositionPolymorphismeOnPathLow[comptPol]][5])-1
                                nucleoRefLow=self.dicoCloseSNPLow[listPositionPolymorphismeOnPathLow[comptPol]][1]
                                table[1]=positionSnpLow
                                table[3]=nucleoLow
                                table[4]=nucleoUp
                                VCFObject.nucleoRef.append([nucleoRefLow,positionSnpLow])
                                tablebis.append(list(table))
                        tablebis=sorted(tablebis, key=lambda colonnes: colonnes[1])
                        return (tablebis)
                                    
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------                        
         
        def FillVCF(self,VCFfile,nbGeno,table,VCFObject):
                """print the VCFFile for each line of close snps"""
                #ID=1
                subIDs = range(1,len(table)+1,1) #subIDs for the different SNPs of a given close bubble : ex: 454_1, 454_2 and 454_3 for 3 SNPs inside the bubble of ID 454
                if VCFObject.reverse == "-1":
                        # if the bubble of close SNPs is mapped on reverse strand, their subIDs are reversed, this way the subID always correspond to the order of apparition of the SNP in the bubble path
                        subIDs = range(len(table),0,-1)
                i=0
                nucleoRef=None
                if VCFObject.chrom=="*":
                        table[line][0]=self.listSam[0].split("_")[0]
                for line in range(len(table)):
                        for i in range(len(VCFObject.nucleoRef)):
                                if table[line][1] in VCFObject.nucleoRef[i]:
                                        nucleoRef=VCFObject.nucleoRef[i][0]   
                        table[line][0]=VCFObject.chrom
                        table[line][2]=str(self.variantID)+"_"+str(subIDs[line])
                        table[line][5]="."
                        table[line][6]=VCFObject.filterField
                        table[line][7]=f"Ty{VCFObject.variantType};Rk={self.rank};UL={self.len_unitig_left};UR={self.len_unitig_right};CL={self.contigLeft};CR={self.contigRight};Genome={nucleoRef};Sd={VCFObject.reverse}"
                        if VCFObject.filterField=="MULTIPLE" and VCFObject.XA:
                                table[line][7]+=f";XA={VCFObject.XA}"
                        #TODO: eviter ces "replace"
                        # table[line][7]=table[line][7].replace("None",".") # done during PrintOneLine
                        table[line][7]=table[line][7].replace("none",".")
                        table[line][7]=table[line][7].replace("=;","=.;")
                        table[line][8]=VCFObject.formatField
                        table[line][9]=VCFObject.genotypes
                        #ID+=1
                        i+=1
                error=VCFObject.CheckOutputConsistency(table,self)
                if error == 0: 
                        for l in range(len(table)):
                                VCFObject.PrintOneLine(table[l],VCFfile)        
        
        
#############################################################################################
#############################################################################################        
class VCFFIELD():
        def __init__(self):
                ##VCF Fields
                self.filterField=None
                self.variantType=None
                self.phased=None #phased genotype
                self.formatField=None 
                self.genotypes="" #genotype field =>put it in the vcf
                self.chrom=""
                self.ref=""
                self.alt=""
                self.qual=""
                self.nucleoRef=None
                self.reverse=""
                self.XA=None
           
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------    
        
        def PrintOneLine(self,table,VCF):
                """Prints the line of the current SNP in the VCF file."""
                if table==[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]:
                        return()
                for i in range(len(table)):
                        element=table[i]
                        element=str(element).replace("None",".") # TODO: peut on éviter ce nouveau 'replace'... ?
                        VCF.write((str(element)).strip())
                        if i<len(table)-1 and table[i+1]!="": VCF.write("\t")
                VCF.write('\n')
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------    
                
        def CheckOutputConsistency(self,table,VARIANT):
                """Checks if an error occured during variant treatement"""
                current_position=None
                previous_position=None
                error=0
                try:#Case of SNPs CLOSE
                        for line in len(table): # ATTENTION BUG ICI: CE 'FOR' NE FAIT RIEN (for line in range(len(table)) fait qq chose. J'ai essaye (pierre 22 juin 2016) mais ça leve une des erreurs.
                                # Test if positions follow each other
                                current_position=int(table[line][1])
                                if previous_position:
                                        if previous_position<current_position:
                                                error+=0
                                        else:
                                                sys.stderr.write("!!! an error occurred in determining the position of close snps !!!\n")
                                                error+=1
                                previous_position=current_position
                        if "SNP" in table[0][1] and table[0][6]=="PASS":
                                        sys.stderr.write("!!! an error occurred in determining the filter of close snps (an unmapped SNP is \"PASS\")!!!\n")
                                        error+=1
                        if VARIANT.upper_path.boolRef==None or VARIANT.lower_path.boolRef==None:
                                sys.stderr.write("!!! Impossible to determine if path are identical to the reference or not (check cigarcode or ReferenceChecker) !!!\n")
                                error+=1
                except(TypeError,IndexError): # Case of SNP and INDEL
                        if "SNP" in table[0] and table[6]=="PASS":
                                sys.stderr.write("!!! an error occurred in determining the filter of close snps (an unmapped SNP is \"PASS\")!!!\n")
                                error+=1
                        if "INDEL" in table[0] and table[6]=="PASS":
                                sys.stderr.write("!!! an error occurred in determining the filter of indel (an unmapped INDEL is \"PASS\")!!!\n")
                                error+=1
                        if VARIANT.upper_path.boolRef==None or VARIANT.lower_path.boolRef==None:
                                sys.stderr.write("!!! Impossible to determine if path are identical to the reference or not (check cigarcode or ReferenceChecker) !!!\n")
                                error+=1
                if error>0:
                        sys.stderr.write(" !!! Line where the error occurred !!!\n")
                        sys.stderr.write(str(VARIANT.upper_path.listSam)+"\n")
                        sys.stderr.write(str(VARIANT.lower_path.listSam)+"\n")
                else : return (error)     
