Haplotyper

A reference-free exact haplotyper for multiple strains.

For the error rate experiment, see experiments/error_rate/error_rate_experiment_discosnp.sh and experiments/error_rate/error_rate_experiment_simulated.sh

For the read length experiment, see experiments/read_length/generate_all_testdatas.sh

Name		Name	Last commit message	Last commit date
Latest commit History 35 Commits
experiments		experiments
.gitignore		.gitignore
active_rows.cpp		active_rows.cpp
brute_force_mapper.cpp		brute_force_mapper.cpp
c1p_solver.cpp		c1p_solver.cpp
collapse_multiples.cpp		collapse_multiples.cpp
evaluate_merge_success.cpp		evaluate_merge_success.cpp
fasta_utils.cpp		fasta_utils.cpp
fasta_utils.h		fasta_utils.h
find_snps.cpp		find_snps.cpp
haplotyper.cpp		haplotyper.cpp
haplotyper.h		haplotyper.h
haplotyper_main.cpp		haplotyper_main.cpp
haplotyper_test.cpp		haplotyper_test.cpp
identify_outliers.cpp		identify_outliers.cpp
make_reads.cpp		make_reads.cpp
make_snps.cpp		make_snps.cpp
matrix_bander.cpp		matrix_bander.cpp
merge_similars.cpp		merge_similars.cpp
merge_subsets.cpp		merge_subsets.cpp
mutate_snpsupports.cpp		mutate_snpsupports.cpp
permutate_snpsupports.cpp		permutate_snpsupports.cpp
prettify_sort.cpp		prettify_sort.cpp
proper_active_rows_per_snp.cpp		proper_active_rows_per_snp.cpp
readme.md		readme.md
remove_outliers.cpp		remove_outliers.cpp
remove_zero_columns.cpp		remove_zero_columns.cpp
renumberer.cpp		renumberer.cpp
reposition_reads.cpp		reposition_reads.cpp
simulate_SNPfinding.cpp		simulate_SNPfinding.cpp
switch_distance_scorer.cpp		switch_distance_scorer.cpp
variant_utils.cpp		variant_utils.cpp
variant_utils.h		variant_utils.h
verify_result.cpp		verify_result.cpp
visualize_snpsupport.cpp		visualize_snpsupport.cpp

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