xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-02 10:08:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

expose purge_dups

Browse Source
This commit is contained in:
chhylp123
2020-04-18 00:45:47 -04:00
parent 85c57fd087
commit 7f6725ead3
6 changed files with 117 additions and 36 deletions
Download Patch File Download Diff File Expand all files Collapse all files
CommandLines.cpp
+37 -3
View File
@@ -15,7 +15,6 @@ static ko_longopt_t long_options[] = {
{ "write-paf", ko_no_argument, 302 },
{ "write-ec", ko_no_argument, 303 },
{ "skip-triobin", ko_no_argument, 304 },
{ "purge-trio", ko_no_argument, 305 },
{ 0, 0, 0 }
};
@@ -58,6 +57,15 @@ void Print_H(hifiasm_opt_t* asm_opt)
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, " Purge-dups:\n");
fprintf(stderr, " -l INT level of purge-dup. In default, [%d] for non-trio; [%d] for trio (see hifiasm.1 for details)\n",
asm_opt->purge_level_primary, asm_opt->purge_level_trio);
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",
asm_opt->purge_overlap_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");
}
@@ -97,6 +105,10 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->max_short_tip = 3;
asm_opt->min_cnt = 2;
asm_opt->mid_cnt = 5;
asm_opt->purge_level_primary = 2;
asm_opt->purge_level_trio = 0;
asm_opt->purge_simi_rate = 0.75;
asm_opt->purge_overlap_len = 1;
}
void destory_opt(hifiasm_opt_t* asm_opt)
@@ -259,6 +271,19 @@ int check_option(hifiasm_opt_t* asm_opt)
return 0;
}
if(asm_opt->purge_level_primary < 0 || asm_opt->purge_level_primary > 2)
{
fprintf(stderr, "[ERROR] the level of purge-dup should be [0, 2] (-l)\n");
return 0;
}
if(ha_opt_triobin(asm_opt) && ((asm_opt->purge_level_trio < 0 || asm_opt->purge_level_trio > 1)))
{
fprintf(stderr, "[ERROR] the level of purge-dup for trio should be [0, 1] (-l)\n");
return 0;
}
if(asm_opt->fn_bin_yak[0] != NULL && check_file(asm_opt->fn_bin_yak[0], "YAK1") == 0) return 0;
if(asm_opt->fn_bin_yak[1] != NULL && check_file(asm_opt->fn_bin_yak[1], "YAK2") == 0) return 0;
@@ -280,6 +305,10 @@ int check_option(hifiasm_opt_t* asm_opt)
// fprintf(stderr, "small removed unitig threshold: %d\n", asm_opt->max_short_tip);
// fprintf(stderr, "min_cnt: %d\n", asm_opt->min_cnt);
// fprintf(stderr, "mid_cnt: %d\n", asm_opt->mid_cnt);
// fprintf(stderr, "purge_level_primary: %d\n", asm_opt->purge_level_primary);
// fprintf(stderr, "purge_level_trio: %d\n", asm_opt->purge_level_trio);
// fprintf(stderr, "purge_simi_rate: %f\n", asm_opt->purge_simi_rate);
// fprintf(stderr, "purge_overlap_len: %d\n", asm_opt->purge_overlap_len);
return 1;
}
@@ -317,7 +346,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
int c;
while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:w:m:n:r:a:b:z:x:y:p:c:d:M:P:if:D:FN:1:2:3:4:", long_options)) >= 0) {
while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:w:m:n:r:a:b:z:x:y:p:c:d:M:P:if:D:FN:1:2:3:4:l:s:O:", long_options)) >= 0) {
if (c == 'h')
{
Print_H(asm_opt);
@@ -356,7 +385,12 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 302) asm_opt->flag |= HA_F_WRITE_PAF;
else if (c == 303) asm_opt->flag |= HA_F_WRITE_EC;
else if (c == 304) asm_opt->flag |= HA_F_SKIP_TRIOBIN;
else if (c == 305) asm_opt->flag |= HA_F_PURGE_TRIO;
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);
}
else if (c == 's') asm_opt->purge_simi_rate = atof(opt.arg);
else if (c == 'O') asm_opt->purge_overlap_len = atoll(opt.arg);
else if (c == ':')
{
fprintf(stderr, "[ERROR] missing option argument in \"%s\"\n", argv[opt.i - 1]);