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for high-het and coverage

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chhylp123
2020-07-28 13:07:35 -04:00
parent 94008c02ac
commit ace34ae2b8
12 changed files with 1902 additions and 89 deletions
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6
CommandLines.cpp
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@@ -23,6 +23,7 @@ static ko_longopt_t long_options[] = {
{ "ex-iter", ko_required_argument, 308 },
{ "purge-cov", ko_required_argument, 309 },
{ "pri-range", ko_required_argument, 310 },
{ "high-het", ko_no_argument, 311 },
{ 0, 0, 0 }
};
@@ -77,6 +78,8 @@ void Print_H(hifiasm_opt_t* asm_opt)
asm_opt->purge_overlap_len);
fprintf(stderr, " --purge-cov INT\n");
fprintf(stderr, " coverage upper bound of Purge-dups [auto]\n");
fprintf(stderr, " --high-het enable this mode for high heterozygosity sample\n");
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");
@@ -433,7 +436,8 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
{
asm_opt->recover_atg_cov_min = asm_opt->recover_atg_cov_max = -1;
}
}
}
else if (c == 311) asm_opt->flag |= HA_F_HIGH_HET;
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);