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purge_dups for high het

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chhylp123
2021-03-08 20:52:11 -05:00
parent e8b92f7a40
commit 8aa87fdce8
8 changed files with 2766 additions and 1765 deletions
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CommandLines.cpp
+3 -3
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@@ -89,7 +89,7 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " -4 FILE list of hap2/maternal read names []\n");
fprintf(stderr, " Purge-dups:\n");
fprintf(stderr, " -l INT purge level. 0: no purging; 1: light; 2: aggressive [0 for trio; 2 for unzip]\n");
fprintf(stderr, " -l INT purge level. 0: no purging; 1: light; 2/3: aggressive [0 for trio; 2 for unzip]\n");
fprintf(stderr, " -s FLOAT similarity threshold for duplicate haplotigs [%g]\n",
asm_opt->purge_simi_rate);
fprintf(stderr, " -O INT min number of overlapped reads for duplicate haplotigs [%d]\n",
@@ -360,9 +360,9 @@ int check_option(hifiasm_opt_t* asm_opt)
return 0;
}
if(asm_opt->purge_level_primary < 0 || asm_opt->purge_level_primary > 2)
if(asm_opt->purge_level_primary < 0 || asm_opt->purge_level_primary > 3)
{
fprintf(stderr, "[ERROR] the level of purge-dup should be [0, 2] (-l)\n");
fprintf(stderr, "[ERROR] the level of purge-dup should be [0, 3] (-l)\n");
return 0;
}