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update for r350

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chhylp123
2021-07-26 00:16:00 -04:00
parent b14f894160
commit 321acb2d8a
12 changed files with 241 additions and 130 deletions
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12
CommandLines.cpp
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@@ -66,16 +66,16 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " -D FLOAT drop k-mers occurring >FLOAT*coverage times [%.1f]\n", asm_opt->high_factor);
fprintf(stderr, " -N INT consider up to max(-D*coverage,-N) overlaps for each oriented read [%d]\n", asm_opt->max_n_chain);
fprintf(stderr, " -r INT round of correction [%d]\n", asm_opt->number_of_round);
fprintf(stderr, " -z INT length of adapters that should be removed [%d]\n", asm_opt->adapterLen);
fprintf(stderr, " Assembly:\n");
fprintf(stderr, " -a INT round of assembly cleaning [%d]\n", asm_opt->clean_round);
fprintf(stderr, " -z INT length of adapters that should be removed [%d]\n", asm_opt->adapterLen);
fprintf(stderr, " -m INT pop bubbles of <INT in size in contig graphs [%lld]\n", asm_opt->large_pop_bubble_size);
fprintf(stderr, " -p INT pop bubbles of <INT in size in unitig graphs [%lld]\n", asm_opt->small_pop_bubble_size);
fprintf(stderr, " -n INT remove tip unitigs composed of <=INT reads [%d]\n", asm_opt->max_short_tip);
fprintf(stderr, " -x FLOAT max overlap drop ratio [%.2g]\n", asm_opt->max_drop_rate);
fprintf(stderr, " -y FLOAT min overlap drop ratio [%.2g]\n", asm_opt->min_drop_rate);
fprintf(stderr, " -i ignore saved read correction and overlaps\n");
fprintf(stderr, " -u disable post join contigs step which may improve N50\n");
fprintf(stderr, " -u disable post-join step for contigs which may improve N50\n");
fprintf(stderr, " --hom-cov INT\n");
fprintf(stderr, " homozygous read coverage [auto]\n");
fprintf(stderr, " --lowQ INT\n");
@@ -95,12 +95,12 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " Trio-partition:\n");
fprintf(stderr, " -1 FILE hap1/paternal k-mer dump generated by \"yak count\" []\n");
fprintf(stderr, " -2 FILE hap2/maternal k-mer dump generated by \"yak count\" []\n");
fprintf(stderr, " -3 FILE list of hap1/paternal read names []\n");
fprintf(stderr, " -4 FILE list of hap2/maternal read names []\n");
fprintf(stderr, " -c INT lower bound of the binned k-mer's frequency [%d]\n", asm_opt->min_cnt);
fprintf(stderr, " -d INT upper bound of the binned k-mer's frequency [%d]\n", asm_opt->mid_cnt);
fprintf(stderr, " -3 FILE list of hap1/paternal read names []\n");
fprintf(stderr, " -4 FILE list of hap2/maternal read names []\n");
fprintf(stderr, " --t-occ INT\n");
fprintf(stderr, " force remove unitigs with >INT unexpected haplotype-specific reads;\n");
fprintf(stderr, " forcedly remove unitigs with >INT unexpected haplotype-specific reads;\n");
fprintf(stderr, " ignore graph topology; [%d]\n", asm_opt->trio_flag_occ_thres);
fprintf(stderr, " Purge-dups:\n");
@@ -131,7 +131,7 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " detect misjoined unitigs of >=INT in size; 0 to disable [%lu]\n", asm_opt->misjoin_len);
fprintf(stderr, "Example: ./hifiasm -o NA12878.asm -t 32 NA12878.fq.gz\n");
fprintf(stderr, "See `man ./hifiasm.1' for detailed description of these command-line options.\n");
fprintf(stderr, "See `https://hifiasm.readthedocs.io/en/latest/' or `man ./hifiasm.1' for complete documentation.\n");
}
void init_opt(hifiasm_opt_t* asm_opt)