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Release minimap2-2.25 (r1173)

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This commit is contained in:
Heng Li
2023-04-25 12:44:52 -04:00
parent f1b3c7ad06
commit 4483f89ee5
13 changed files with 52 additions and 74 deletions
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main.c
+2 -4
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@@ -120,7 +120,7 @@ static inline void yes_or_no(mm_mapopt_t *opt, int64_t flag, int long_idx, const
int main(int argc, char *argv[])
{
const char *opt_str = "2aSDw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:LC:yYPo:e:U:j:J:";
const char *opt_str = "2aSDw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:LC:yYPo:e:U:J:";
ketopt_t o = KETOPT_INIT;
mm_mapopt_t opt;
mm_idxopt_t ipt;
@@ -152,8 +152,7 @@ int main(int argc, char *argv[])
o = KETOPT_INIT;
while ((c = ketopt(&o, argc, argv, 1, opt_str, long_options)) >= 0) {
if (c == 'w') ipt.w = atoi(o.arg), ipt.flag &= ~MM_I_SYNCMER;
else if (c == 'j') ipt.w = atoi(o.arg), ipt.flag |= MM_I_SYNCMER;
if (c == 'w') ipt.w = atoi(o.arg);
else if (c == 'k') ipt.k = atoi(o.arg);
else if (c == 'H') ipt.flag |= MM_I_HPC;
else if (c == 'd') fnw = o.arg; // the above are indexing related options, except -I
@@ -329,7 +328,6 @@ int main(int argc, char *argv[])
fprintf(fp_help, " -H use homopolymer-compressed k-mer (preferrable for PacBio)\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, " -j INT syncmer submer size (overriding -w) []\n");
fprintf(fp_help, " -I NUM split index for every ~NUM input bases [8G]\n");
fprintf(fp_help, " -d FILE dump index to FILE []\n");
fprintf(fp_help, " Mapping:\n");