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upadate man-page and readme

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Haoyu Cheng
2020-01-04 11:54:08 +08:00
parent 1e46798bfb
commit d8416873f3
7 changed files with 407 additions and 176 deletions
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Assembly.cpp
+7 -8
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@@ -1918,10 +1918,10 @@ void generate_overlaps(int last_round)
Output_PAF();
build_string_graph_without_clean(MIN_OVERLAP_COVERAGE, R_INF.paf, R_INF.reverse_paf,
R_INF.total_reads, R_INF.read_length, MIN_OVERLAP_LEN, MAX_HANG_LEN, asm_opt.clean_round,
asm_opt.pop_bubble_size, asm_opt.min_drop_rate, asm_opt.max_drop_rate, asm_opt.output_file_name,
MAX_BUBBLE_DIST, 0, 1);
build_string_graph_without_clean(asm_opt.min_overlap_coverage, R_INF.paf, R_INF.reverse_paf,
R_INF.total_reads, R_INF.read_length, asm_opt.min_overlap_Len, asm_opt.max_hang_Len, asm_opt.clean_round,
asm_opt.gap_fuzz, asm_opt.min_drop_rate, asm_opt.max_drop_rate, asm_opt.output_file_name,
asm_opt.large_pop_bubble_size, 0, 1);
}
@@ -1931,10 +1931,9 @@ void Correct_Reads(int last_round)
if(asm_opt.load_index_from_disk && load_all_data_from_disk(&R_INF.paf, &R_INF.reverse_paf,
asm_opt.output_file_name))
{
build_string_graph_without_clean(MIN_OVERLAP_COVERAGE, R_INF.paf, R_INF.reverse_paf,
R_INF.total_reads, R_INF.read_length, MIN_OVERLAP_LEN, MAX_HANG_LEN, asm_opt.clean_round,
asm_opt.pop_bubble_size, asm_opt.min_drop_rate, asm_opt.max_drop_rate,
asm_opt.output_file_name, MAX_BUBBLE_DIST, 0, 0);
build_string_graph_without_clean(asm_opt.min_overlap_coverage, R_INF.paf, R_INF.reverse_paf,
R_INF.total_reads, R_INF.read_length, asm_opt.min_overlap_Len, asm_opt.max_hang_Len, asm_opt.clean_round,
asm_opt.gap_fuzz, asm_opt.min_drop_rate, asm_opt.max_drop_rate, asm_opt.output_file_name, asm_opt.large_pop_bubble_size, 0, 0);
exit(1);
}
else