; = HAMMER =
; input options: working dir, input files, offset, and possibly kmers
input_working_dir			/home/snikolenko/algorithmic-biology/assembler/build/release/hammer/test_dir
input_paired				1
input_paired_1				/home/snikolenko/data/reads.input.0.head
input_paired_2				/home/snikolenko/data/reads.input.1.head
input_single				
input_trim_quality			2
input_gzipped				1
input_qvoffset				64
input_read_solid_kmers		0
input_solid_kmers			/home/snikolenko/algorithmic-biology/assembler/build/release/hammer/test_dir/00.kmers.result

; == HAMMER GENERAL ==
; general options
general_do_everything_after_first_iteration	1
general_reconstruct_only	1
general_change_n_to_a		0
general_hard_memory_limit	15
general_max_nthreads		4
general_tau					1
general_gzip				0
general_max_iterations		2
general_blob_margin			0.25
general_gzip_margin			4.0
general_file_buffer_exp		20
general_common_quality		-1
general_debug	0
general_minimizers			1			
general_num_minimizers		5

; count k-mers
count_do					1
count_numfiles				16
count_merge_nthreads		4
count_split_buffer			100000

; sort k-mers
sort_do						1

; extract and sort subvectors
subvectors_do								1
subvectors_blocksize_quadratic_threshold	50

; hamming graph clustering
hamming_do					1
hamming_write_solid_kmers	0
hamming_write_bad_kmers		0
hamming_class_buffer		100000

; bayesian subclustering
bayes_do						1
bayes_nthreads					1
bayes_quality_threshold			0.995
bayes_singleton_threshold		0.995
bayes_nonsingleton_threshold	0.5
bayes_use_hamming_dist			0
bayes_discard_only_singletons	0
bayes_debug_output				0
bayes_hammer_mode				0

; iterative expansion step
expand_do					1
expand_max_iterations		5
expand_nthreads				6
expand_write_each_iteration	0
expand_write_kmers_result	1

; read correction
correct_do					1
correct_discard_bad			0
correct_use_threshold		1
correct_threshold			0.98
correct_nthreads			8
correct_readbuffer			100000




