From 10622c882ea77e2c38c88b293513f2874c47a2da Mon Sep 17 00:00:00 2001 From: Chirag Jain Date: Thu, 13 Jun 2024 05:30:04 -0700 Subject: [PATCH] Added -I option back, address #40 --- src/main.c | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/main.c b/src/main.c index 89c147c..f6e46cd 100644 --- a/src/main.c +++ b/src/main.c @@ -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; @@ -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; @@ -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");