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keeping more telomeres

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chhylp123
2024-05-06 04:02:20 -04:00
parent 73dd5eeb5b
commit 70fd9a0b1f
6 changed files with 570 additions and 117 deletions
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46
CommandLines.cpp
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@@ -66,6 +66,11 @@ static ko_longopt_t long_options[] = {
{ "scaf-gap", ko_required_argument, 351},
{ "sec-in", ko_required_argument, 352},
{ "somatic-cov", ko_required_argument, 353},
{ "telo-m", ko_required_argument, 354},
{ "telo-p", ko_required_argument, 355},
{ "telo-d", ko_required_argument, 356},
{ "telo-s", ko_required_argument, 357},
{ "ctg-n", ko_required_argument, 358},
// { "path-round", ko_required_argument, 348},
{ 0, 0, 0 }
};
@@ -121,6 +126,9 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " break contigs at positions with <=FLOAT*coverage exact overlaps;\n");
fprintf(stderr, " only work with '--b-cov' or '--h-cov'[%.2f]\n", asm_opt->m_rate);
fprintf(stderr, " --primary output a primary assembly and an alternate assembly\n");
fprintf(stderr, " --ctg-n INT\n");
fprintf(stderr, " remove tip contigs composed of <=INT reads [%d]\n", asm_opt->max_contig_tip);
// fprintf(stderr, " --pri-range INT1[,INT2]\n");
// fprintf(stderr, " keep contigs with coverage in this range in p_ctg.gfa; -1 to disable [auto,inf]\n");
@@ -188,6 +196,17 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " --scaf-gap INT\n");
fprintf(stderr, " max gap size for scaffolding [%ld]\n", asm_opt->self_scaf_gap_max);
fprintf(stderr, " Telomere-identification:\n");
fprintf(stderr, " --telo-m STR\n");
fprintf(stderr, " telomere motif at 5'-end; CCCTAA for human [%s]\n", ((asm_opt->telo_motif)?(asm_opt->telo_motif):("NULL")));///5'-end, check CCCTAA
fprintf(stderr, " --telo-p INT\n");
fprintf(stderr, " non-telomeric penalty [%ld]\n", asm_opt->telo_pen);
fprintf(stderr, " --telo-d INT\n");
fprintf(stderr, " max drop [%ld]\n", asm_opt->telo_drop);
fprintf(stderr, " --telo-s INT\n");
fprintf(stderr, " min score for telomere reads [%ld]\n", asm_opt->telo_mic_sc);
fprintf(stderr, "Example: ./hifiasm -o NA12878.asm -t 32 NA12878.fq.gz\n");
fprintf(stderr, "See `https://hifiasm.readthedocs.io/en/latest/' or `man ./hifiasm.1' for complete documentation.\n");
}
@@ -244,6 +263,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->min_overlap_coverage = 0;
asm_opt->max_short_tip = 3;
asm_opt->max_short_ul_tip = 6;
asm_opt->max_contig_tip = 3;
asm_opt->min_cnt = 2;
asm_opt->mid_cnt = 5;
asm_opt->purge_level_primary = 3;
@@ -309,6 +329,11 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->self_scaf_gap_max = 3000000;
asm_opt->sec_in = NULL;
asm_opt->somatic_cov = -1;
asm_opt->telo_motif = NULL;
asm_opt->telo_pen = 1;
asm_opt->telo_drop = 2000;
asm_opt->telo_mic_sc = 500;
}
void destory_enzyme(enzyme* f)
@@ -638,6 +663,22 @@ int check_option(hifiasm_opt_t* asm_opt)
return 0;
}
if(asm_opt->telo_motif) {
uint64_t k, tlen = strlen((asm_opt->telo_motif)); char c;
if(tlen > 32) {
fprintf(stderr, "[ERROR] [--telo-m] must be no longer than 32\n");
return 0;
}
for (k = 0; k < tlen; k++) {
c = asm_opt->telo_motif[k];
if(c != 'A' && c != 'C' && c != 'G' && c != 'T' &&
c != 'a' && c != 'c' && c != 'g' && c != 't') {
fprintf(stderr, "[ERROR] [--telo-m] must be A/C/G/T\n");
return 0;
}
}
}
return 1;
}
@@ -859,6 +900,11 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 351) asm_opt->self_scaf_gap_max = atol(opt.arg);
else if (c == 352) get_hic_enzymes(opt.arg, &(asm_opt->sec_in), 0);
else if (c == 353) asm_opt->somatic_cov = atol(opt.arg);
else if (c == 354) asm_opt->telo_motif = opt.arg;
else if (c == 355) asm_opt->telo_pen = atol(opt.arg);
else if (c == 356) asm_opt->telo_drop = atol(opt.arg);
else if (c == 357) asm_opt->telo_mic_sc = atol(opt.arg);
else if (c == 358) asm_opt->max_contig_tip = atol(opt.arg);
else if (c == 'l') { ///0: disable purge_dup; 1: purge containment; 2: purge overlap
asm_opt->purge_level_primary = asm_opt->purge_level_trio = atoi(opt.arg);
}