--build  build.txt                 #####file name for the build file#####
--noCopies  2                        #####2: non-internal phasing, the number of chromosome (ploidy): for internal phasing#####
--maxIndiv	100000                 #####the number of individuals included for analysis#####
--phasingType 1                      #####0: non-internal phasing; 1: internal phasing #####
--numRep        10                    #####number of replications of the EM algorithm with different start values#####


###################################################################################################
#####The following parameters usually don't have to change. They are realted to the flow    #######
#####of the program and initial values. If you are intersted in these parameters, please    #######
#####contact Dr. Lachlan Coin (l.coin@imperial.ac.uk).                                      #######
###################################################################################################

--inputGenotype genotypeInfo.txt     #####input genotype file#####
--inputSample sampleID.txt           #####input sample id file#####
###--mid 2:12:2400                      #####chromsome name: start snp position: end snp position#####

--modify0Internal       1:1:1:1:1:1:1:1      #####number the ancestral haplotypes (one of '1' correspoinds to one state. This example has 8 ancestral halotypes)#####
--modify0nonInternal       0:1:1:1:1:2:2:2:2     #####number the ancestral haplotypes 0:deletion; 1: oneCopy; 2:twoCopy)#####
--transMode0Internal                    2   
--transMode0nonInternal	     4:0:4 
--modelCNPInternal                      2  ##number of different alleles, such as A and B
--modelCNPnonInternal                      6
--modifyFrac0           0.125 

--weights 1
--format geno
--phenToPlot population
--numIteForHap  0   ##number of privious 10 iteration only for training haplotype
--loess false
--median_correction false
--summarise                     true
--writeHMM                      0   
--numIt               25             #####number of iterations for each EM algorithm#####
--noSamplesFromHMM       100         #####number of samples from posterior distribution#####

--distanceLD 0                       #####calcualte LD within a specific distance bp#####   
--r_state_var_mod	1.0
--type        					deletion
--onlyCopyNo                    false  
--expModelIntHotSpot            1:1:1

--backgroundCount 2
--restrictKb 					0:0

--missingRate 0
--baseDir 
--inputDir  

--r_state_mean					0.0				
--r_state_var					0.08
--r_state_skew					0	
--r_prior						1	
--scoreDT  true
--trans1                        false  		        
--modifyWithData                0                  
--u_global                      1:1:1e5:1e5        
--u_global1                     1:1:1e5:1e5     	
--samplePermute					0									
--runFastPhase                  false
--keepSamples                   false
--run true
--realRandom true
--r_train 1e8
--b_train 1e8
--trainCGH false
--b_mean   0.00:0.25:1/3:0.5:2/3:0.75:1.00
--b_var    0.05:0.05:0.05:0.05:0.05:0.05:0.05 
--b_skew   1e10:-0.5:-1.0:0.00:1.0:0.5:^-1e10
--r_x       0.0:0.5:1.0:1.5:2.0:3.0:4.0
--r_var     0.1:0.1:0.1:0.1:0.1:0.1:0.1
--r_skew    ^-2:^-2:1e-3:2:2:2:2
--r_mean   ^-1.1:^-0.53:0:0.35:0.54:1.09:1.38
--frac  0.8:0.8:0.8:0.8:1.0
--start 0.1:0.1:0.1:10:1e-5                   
--limit  0.1:0.1:0.1:1:1e-6                   
--index_to_start 0.0:0.0:0.0:0.0:0.0
--freq_update 0:0:0:0:0
--meanvarskewprior 100:100:0.1
--drop false
--softenHapMap  0.12
--cn_ratio  1.0
--codesToRestrict x     
--keepBest false
--resample false
--saveStatePath true
--allowCloning false
--topBottom false
--plot 0
--logplot true
--trainEnsemble 2
--cnStatesInCommonClass 1
--numThreads 1
--supressR  false
--supressB  false
--toDel 

