zzh
/
minimap2
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

r1162: fixed a typo; also increased splice pen 

Now slightly better on ISO-seq
This commit is contained in:
Heng Li 2023-04-07 01:19:18 -04:00
parent 1834b1fd42
commit ea2042a577
2 changed files with 14 additions and 14 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
ksw2_exts2_sse.c
View File

@ -123,7 +123,7 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
int sp[4]; int sp[4];
if (flag & KSW_EZ_SPLICE_CMPLX) { if (flag & KSW_EZ_SPLICE_CMPLX) {
for (t = 0; t < 4; ++t) for (t = 0; t < 4; ++t)
sp[t] = (int)((double)sp0[t] / 4. + .499); sp[t] = (int)((double)sp0[t] / 3. + .499);
} else { } else {
sp[0] = flag&KSW_EZ_SPLICE_FLANK? noncan / 2 : 0; sp[0] = flag&KSW_EZ_SPLICE_FLANK? noncan / 2 : 0;
sp[1] = sp[2] = sp[3] = noncan; sp[1] = sp[2] = sp[3] = noncan;
@ -154,7 +154,7 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
} else if (flag & KSW_EZ_SPLICE_REV) { } else if (flag & KSW_EZ_SPLICE_REV) {
if (target[t-1] == 0 && target[t] == 1) // .AC| (revcomp of |GT.) if (target[t-1] == 0 && target[t] == 1) // .AC| (revcomp of |GT.)
z = target[t-2] == 1 || target[t-2] == 3? -1 : 0; // yAC| or not z = target[t-2] == 1 || target[t-2] == 3? -1 : 0; // yAC| or not
else if (target[t-1] == 1 && target[t] == 2) z = 1; // .CG| (revcomp of |GC.) else if (target[t-1] == 2 && target[t] == 1) z = 1; // .GC| (revcomp of |GC.)
else if (target[t-1] == 0 && target[t] == 3) z = 2; // .AT| (revcomp of |AT.) else if (target[t-1] == 0 && target[t] == 3) z = 2; // .AT| (revcomp of |AT.)
} }
((int8_t*)acceptor)[t] = z < 0? 0 : -sp[z]; ((int8_t*)acceptor)[t] = z < 0? 0 : -sp[z];
@ -179,12 +179,12 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
if (flag & KSW_EZ_SPLICE_FOR) { if (flag & KSW_EZ_SPLICE_FOR) {
if (target[t-1] == 3 && target[t] == 2) // .TG| (rev of |GT.) if (target[t-1] == 3 && target[t] == 2) // .TG| (rev of |GT.)
z = target[t-2] == 0 || target[t-2] == 2? -1 : 0; z = target[t-2] == 0 || target[t-2] == 2? -1 : 0;
else if (target[t-1] == 1 && target[t] == 2) z = 1; // .CG| else if (target[t-1] == 1 && target[t] == 2) z = 1; // .CG| (rev of |GC.)
else if (target[t-1] == 3 && target[t] == 0) z = 2; // .TA| else if (target[t-1] == 3 && target[t] == 0) z = 2; // .TA| (rev of |AT.)
} else if (flag & KSW_EZ_SPLICE_REV) { } else if (flag & KSW_EZ_SPLICE_REV) {
if (target[t-1] == 3 && target[t] == 1) // .TC| (comp of .AG|) if (target[t-1] == 3 && target[t] == 1) // .TC| (comp of .AG|)
z = target[t-2] == 0 || target[t-2] == 2? -1 : 0; z = target[t-2] == 0 || target[t-2] == 2? -1 : 0;
else if (target[t-1] == 3 && target[t] == 2) z = 2; // .TG| else if (target[t-1] == 3 && target[t] == 2) z = 2; // .TG| (comp of .AC|)
} }
((int8_t*)acceptor)[t] = z < 0? 0 : -sp[z]; ((int8_t*)acceptor)[t] = z < 0? 0 : -sp[z];
} }

2
minimap.h
View File

@ -5,7 +5,7 @@
#include <stdio.h> #include <stdio.h>
#include <sys/types.h> #include <sys/types.h>
#define MM_VERSION "2.24-r1161-dirty" #define MM_VERSION "2.24-r1162-dirty"
#define MM_F_NO_DIAG 0x001 // no exact diagonal hit #define MM_F_NO_DIAG 0x001 // no exact diagonal hit
#define MM_F_NO_DUAL 0x002 // skip pairs where query name is lexicographically larger than target name #define MM_F_NO_DUAL 0x002 // skip pairs where query name is lexicographically larger than target name