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r421: removed the MM_F_SPLICE_BOTH mode

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In the default splice mode, minimap2 applies two rounds of spliced alignment:
first assuming GT-AG to be the splice signal across all splicing sites and then
assuming CT-AC to be the signal. This is the idea strategy.

In the MM_F_SPLICE_BOTH mode, minimap2 applies one round of spliced alignment,
assuming GT-AG and CT-AC to be the splice signals AT THE SAME TIME. This will
be faster but less accurate. I don't think anyone would like to run minimap2 in
this mode, so I am removing it for clarity.
This commit is contained in:
Heng Li
2017-09-20 11:11:53 -04:00
parent a686461e83
commit 75e6bbc9f6
4 changed files with 14 additions and 21 deletions
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main.c
+5 -6
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@@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.2-r414-dirty"
#define MM_VERSION "2.2-r421-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -124,11 +124,10 @@ int main(int argc, char *argv[])
if (x < 1.0) opt.mid_occ_frac = x, opt.mid_occ = 0;
else opt.mid_occ = (int)(x + .499);
} else if (c == 'u') {
if (*optarg == 'b') opt.flag |= MM_F_SPLICE_FOR|MM_F_SPLICE_REV;
else if (*optarg == 'B') opt.flag |= MM_F_SPLICE_BOTH;
else if (*optarg == 'f') opt.flag |= MM_F_SPLICE_FOR, opt.flag &= ~MM_F_SPLICE_REV;
else if (*optarg == 'r') opt.flag |= MM_F_SPLICE_REV, opt.flag &= ~MM_F_SPLICE_FOR;
else if (*optarg == 'n') opt.flag &= ~(MM_F_SPLICE_FOR|MM_F_SPLICE_REV);
if (*optarg == 'b') opt.flag |= MM_F_SPLICE_FOR|MM_F_SPLICE_REV; // both strands
else if (*optarg == 'f') opt.flag |= MM_F_SPLICE_FOR, opt.flag &= ~MM_F_SPLICE_REV; // match GT-AG
else if (*optarg == 'r') opt.flag |= MM_F_SPLICE_REV, opt.flag &= ~MM_F_SPLICE_FOR; // match CT-AC (reverse complement of GT-AG)
else if (*optarg == 'n') opt.flag &= ~(MM_F_SPLICE_FOR|MM_F_SPLICE_REV); // don't try to match the GT-AG signal
else {
fprintf(stderr, "[E::%s] unrecognized cDNA direction\n", __func__);
return 1;