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r1235: allow --splice and --frag at the same time

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This seems to largely work, though the accuracy is reduced and no pairs are
proper. More investigation needed for practical uses.
This commit is contained in:
Heng Li
2025-03-30 16:32:38 -04:00
parent 54f8e5f7d6
commit ce30004e02
2 changed files with 1 additions and 5 deletions
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4
main.c
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@@ -319,10 +319,6 @@ int main(int argc, char *argv[])
if (*s == ',') opt.e2 = strtol(s + 1, &s, 10);
}
}
if ((opt.flag & MM_F_SPLICE) && (opt.flag & MM_F_FRAG_MODE)) {
fprintf(stderr, "[ERROR]\033[1;31m --splice and --frag should not be specified at the same time.\033[0m\n");
return 1;
}
if (!fnw && !(opt.flag&MM_F_CIGAR))
ipt.flag |= MM_I_NO_SEQ;
if (mm_check_opt(&ipt, &opt) < 0)

2
minimap.h
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@@ -5,7 +5,7 @@
#include <stdio.h>
#include <sys/types.h>
#define MM_VERSION "2.28-r1234-dirty"
#define MM_VERSION "2.28-r1235-dirty"
#define MM_F_NO_DIAG (0x001LL) // no exact diagonal hit
#define MM_F_NO_DUAL (0x002LL) // skip pairs where query name is lexicographically larger than target name