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Merge branch 'master' into splice-model

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This commit is contained in:
Heng Li
2023-04-06 21:09:18 -04:00
parent 85a5260408 a6fab118c5
commit 35732f3025
14 changed files with 365 additions and 16 deletions
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main.c
+6 -5
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@@ -7,8 +7,6 @@
#include "mmpriv.h"
#include "ketopt.h"
#define MM_VERSION "2.24-r1122"
#ifdef __linux__
#include <sys/resource.h>
#include <sys/time.h>
@@ -122,7 +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:";
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;
@@ -154,7 +152,8 @@ 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);
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;
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
@@ -263,7 +262,8 @@ int main(int argc, char *argv[])
} else if (c == 326) { // --dual
yes_or_no(&opt, MM_F_NO_DUAL, o.longidx, o.arg, 0);
} else if (c == 347) { // --rmq
yes_or_no(&opt, MM_F_RMQ, o.longidx, o.arg, 1);
if (o.arg) yes_or_no(&opt, MM_F_RMQ, o.longidx, o.arg, 1);
else opt.flag |= MM_F_RMQ;
} else if (c == 'S') {
opt.flag |= MM_F_OUT_CS | MM_F_CIGAR | MM_F_OUT_CS_LONG;
if (mm_verbose >= 2)
@@ -324,6 +324,7 @@ 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 [4G]\n");
fprintf(fp_help, " -d FILE dump index to FILE []\n");
fprintf(fp_help, " Mapping:\n");