zzh
/
minimap2
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

expose scoring

This commit is contained in:
Heng Li 2017-06-27 21:37:25 -04:00
parent 533150d49d
commit 51057ab673
1 changed files with 13 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

17
main.c
View File

@ -66,7 +66,7 @@ int main(int argc, char *argv[])
mm_realtime0 = realtime();
mm_mapopt_init(&opt);
while ((c = getopt_long(argc, argv, "w:k:t:r:f:Vv:g:I:d:ST:s:x:Hcp:M:n:z:F:", long_options, &long_idx)) >= 0) {
while ((c = getopt_long(argc, argv, "w:k:t:r:f:Vv:g:I:d:ST:s:x:Hcp:M:n:z:F:A:B:O:E:", long_options, &long_idx)) >= 0) {
if (c == 'w') w = atoi(optarg);
else if (c == 'k') k = atoi(optarg);
else if (c == 'H') is_hpc = 1;
@ -83,6 +83,10 @@ int main(int argc, char *argv[])
else if (c == 'T') opt.sdust_thres = atoi(optarg);
else if (c == 'n') opt.min_cnt = atoi(optarg);
else if (c == 's') opt.min_score = atoi(optarg);
else if (c == 'A') opt.a = atoi(optarg);
else if (c == 'B') opt.b = atoi(optarg);
else if (c == 'O') opt.q = atoi(optarg);
else if (c == 'E') opt.e = atoi(optarg);
else if (c == 'z') opt.zdrop = atoi(optarg);
else if (c == 0 && long_idx == 0) bucket_bits = atoi(optarg); // bucket-bits
else if (c == 0 && long_idx == 2) keep_name = 0; // int-rname
@ -109,7 +113,7 @@ int main(int argc, char *argv[])
if (strcmp(optarg, "ava10k") == 0) {
opt.flag |= MM_F_AVA | MM_F_NO_SELF;
opt.min_score = 100;
w = 5;
is_hpc = 1, k = 19, w = 5;
}
}
}
@ -133,9 +137,14 @@ int main(int argc, char *argv[])
fprintf(stderr, " -T INT SDUST threshold; 0 to disable SDUST [%d]\n", opt.sdust_thres);
fprintf(stderr, " -S skip self and dual mappings\n");
fprintf(stderr, " -p FLOAT threshold to output a mapping [%g]\n", opt.pri_ratio);
fprintf(stderr, " -z INT Z-drop score [%d]\n", opt.zdrop);
fprintf(stderr, " -x STR preset (recommended to be applied before other options) []\n");
fprintf(stderr, " ava10k: -Sw5 -L100 -m0 (PacBio/ONT all-vs-all read mapping)\n");
fprintf(stderr, " ava10k: -Hk19 -Sw5 -s100 (PacBio/ONT all-vs-all read mapping)\n");
fprintf(stderr, " Alignment:\n");
fprintf(stderr, " -A INT matching score [%d]\n", opt.a);
fprintf(stderr, " -B INT mismatch penalty [%d]\n", opt.b);
fprintf(stderr, " -O INT gap open penalty [%d]\n", opt.q);
fprintf(stderr, " -E INT gap extension penalty; a k-long gap costs {-O}+k*{-E} [%d]\n", opt.e);
fprintf(stderr, " -z INT Z-drop score [%d]\n", opt.zdrop);
fprintf(stderr, " Input/Output:\n");
fprintf(stderr, " -F STR output format: sam or paf [paf]\n");
fprintf(stderr, " -c output CIGAR in PAF\n");