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Added -I option back, address #40
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cjain7 committed Jun 13, 2024
1 parent 1a8c9b0 commit 10622c8
Showing 1 changed file with 3 additions and 2 deletions.
5 changes: 3 additions & 2 deletions src/main.c
Original file line number Diff line number Diff line change
Expand Up @@ -108,7 +108,7 @@ static inline void yes_or_no(mm_mapopt_t *opt, int flag, int long_idx, const cha
int main(int argc, char *argv[])
{
unsetenv((char *)"MALLOC_ARENA_MAX"); //for openmp
const char *opt_str = "2aSDw:W:k:K:t:r:f:Vv:g:G:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:LC:yYPo:";
const char *opt_str = "2aSDw:W:k:K:t:r:f:Vv:g:G:I:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:LC:yYPo:";
ketopt_t o = KETOPT_INIT;
mm_mapopt_t opt;
mm_idxopt_t ipt;
Expand Down Expand Up @@ -172,7 +172,7 @@ int main(int argc, char *argv[])
else if (c == 'B') opt.b = atoi(o.arg);
else if (c == 's') opt.min_dp_max = atoi(o.arg);
else if (c == 'C') opt.noncan = atoi(o.arg);
/*else if (c == 'I') ipt.batch_size = mm_parse_num(o.arg);*/
else if (c == 'I') ipt.batch_size = mm_parse_num(o.arg);
else if (c == 'K') opt.mini_batch_size = (int)mm_parse_num(o.arg);
else if (c == 'R') rg = o.arg;
else if (c == 'h') fp_help = stdout;
Expand Down Expand Up @@ -299,6 +299,7 @@ int main(int argc, char *argv[])
fprintf(fp_help, " -H use homopolymer-compressed k-mer\n");
fprintf(fp_help, " -k INT k-mer size (no larger than 28) [%d]\n", ipt.k);
fprintf(fp_help, " -w INT minimizer window size [%d]\n", ipt.w);
fprintf(fp_help, " -I NUM split index for every ~NUM input bases [4G]\n");
fprintf(fp_help, " -W FILE input file containing list of high frequency k-mers []\n");
fprintf(fp_help, " Mapping:\n");
fprintf(fp_help, " -f FLOAT filter out top FLOAT (<1) fraction of repetitive minimizers [0.0]\n");
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