; working directories, input files...
working_dir		/home/snikolenko/algorithmic-biology/assembler/build/release/hammer/tmp
reads			/home/snikolenko/data/head100000.fastq
paired_reads		0
reads_left		/home/snikolenko/data/head10000.fastq
reads_right		/home/snikolenko/data/head10000.fastq_2

; general parameters
tau			1
quality_offset		64
num_threads		1
num_iterations		1

; reading and writing intermediate data
read_blob_and_kmers			0
write_blob_and_kmers			0
exit_after_writing_blob_and_kmers	0
blob					blob.raw.out
kmers					kmers.raw.out
write_kmers_after_clustering		0
read_kmers_after_clustering		0
kmers_after_clustering			/home/snikolenko/algorithmic-biology/assembler/build/release/hammer/tmp/00.kmers.hash

; internal parameters
error_rate				0.01
blocksize_quadratic_threshold		50
good_cluster_threshold			0.98
blob_margin				0.25
trim_quality				4

; aggressive trimming strategies
trim_left_right				1
use_iterative_reconstruction		1
reconstruction_in_full_iterations	1
iterative_reconstruction_threshold	0.995
regular_threshold_for_correction	1
special_nonsingleton_threshold		0.5
discard_only_singletons			0
max_reconstruction_iterations		10
write_each_iteration_kmers		1

; true likelihood based on quality values
use_true_likelihood			1

; latest developments in memory efficiency
conserve_memory					0
num_of_tmp_files				2
skip_to_clustering				0
skip_to_subvectors				0
unload_blob_before_merge		0

; debug output
debug_output_clustering			0
debug_output_likelihood 		0

; new, "better" clustering that might not work out
likelihood_e_step				1
subtract_simplex_volume			1
change_n_to_random				1