config_5V

% configuration file for the HIVhaplotyper
% prefix
5V_Ill_
% filename of reference sequence (FASTA)
5V_ref_seq.fasta
% do_visualize (1 = true, 0 = false)
1
% filname of the aligned reads (sam format)
Illumina_aln_pairs.sam
% have_true_haplotypes  (1 = true, 0 = false)
1
% filname of the true haplotypes (MSA in FASTA format) (fill in any dummy filename if there is no "true" haplotypes)
5VirusMixReference.fasta
% do_local_analysis  (1 = true, 0 = false) (must be 1 in the first run)
1
% max_reads_in_window;
10000
% entropy_threshold
4e-2
%reconstruction_start
790
%reconstruction_stop
5096
%min_mapping_qual  
30
%min_readlength 
220
%max_gap_fraction (relative to alignment length)
0.05
%min_align_score_fraction (relative to read length)
0.35
%alpha_MN_local (prior parameter for multinomial tables over the nucleotides)
25
%min_overlap_factor (reads must have an overlap with the local reconstruction window of at least this factor times the window size)
0.85
%local_window_size_factor (size of  local reconstruction window relative to the median of the read lengths)
0.7
% max number of clusters (in the truncated Dirichlet process)
25
% MCMC iterations
501
% include deletions (0 = no, 1 = yes)
1