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Add the possibility to look for patterns allowing indels.

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Former-commit-id: 0599c2b0ad16df086dbdb08e491503870d8904be
This commit is contained in:
Eric Coissac
2023-03-20 15:28:24 +07:00
parent 5fbe52368c
commit 27d6c60e25
14 changed files with 674 additions and 219 deletions
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50
pkg/obiapat/apat_search.c
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@@ -23,7 +23,8 @@
#define TOPCURS CursiToTop
#define DOWNREAD ReadiDown
#define KRONECK(x, msk) ((~x & msk) ? 0 : 1)
//#define KRONECK(x, msk) ((~x & msk) ? 0 : 1)
#define KRONECK(x, msk) ((x & msk) ? 0 : 1)
#define MIN(x, y) ((x) < (y) ? (x) : (y))
/* -------------------------------------------- */
@@ -192,8 +193,8 @@ int32_t ManberIndel(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
{
int e, emax, found;
uint32_t pos;
uint32_t smask, cmask, sindx;
uint32_t *pr, r[2 * MAX_PAT_ERR + 2];
patword_t smask, cmask, sindx;
patword_t *pr, r[2 * MAX_PAT_ERR + 2];
uint8_t *data;
StackiPtr *stkpos, *stkerr;
uint32_t end;
@@ -220,6 +221,9 @@ int32_t ManberIndel(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
stkpos = pseq->hitpos + patnum;
stkerr = pseq->hiterr + patnum;
EmptyStacki(stkpos[0]);
EmptyStacki(stkerr[0]);
/* loop on text data */
for (pos = begin ; pos < end ; pos++) {
@@ -256,12 +260,14 @@ int32_t ManberIndel(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
/* -------------------------------------------- */
int32_t ManberAll(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
{
if (ppat->maxerr == 0)
return ManberNoErr(pseq, ppat, patnum, begin, length);
else if (ppat->hasIndel)
if (ppat->maxerr == 0){
return ManberNoErr(pseq, ppat, patnum, begin, length);}
else if (ppat->hasIndel) {
return ManberIndel(pseq, ppat, patnum, begin, length);
else
}
else {
return ManberSub(pseq, ppat, patnum, begin, length);
}
}
@@ -271,11 +277,9 @@ int32_t ManberAll(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
/* (avec substitution obligatoire aux bords) */
/* -------------------------------------------- */
int32_t NwsPatAlign(pseq, ppat, nerr, reslen, reserr)
Seq *pseq;
Pattern *ppat;
int32_t nerr, *reslen, *reserr;
{
int32_t NwsPatAlign(Seq *pseq, Pattern *ppat,
int32_t nerr, int32_t begin,
int32_t *reslen, int32_t *reserr) {
uint8_t *sseq, *px;
int32_t i, j, lseq, lpat, npos, dindel, dsub,
*pc, *pi, *pd, *ps;
@@ -283,7 +287,9 @@ int32_t NwsPatAlign(pseq, ppat, nerr, reslen, reserr)
static int32_t sTab[(MAX_PAT_LEN+MAX_PAT_ERR+1) * (MAX_PAT_LEN+1)];
lseq = pseq->seqlen;
lpat = ppat->patlen;
lseq = MIN(lpat + MAX_PAT_ERR+1, pseq->seqlen - begin);
sseq = pseq->data + begin - 1;
pc = sTab; /* |----|----| --> i */
pi = pc - 1; /* | ps | pd | | */
@@ -291,36 +297,39 @@ int32_t NwsPatAlign(pseq, ppat, nerr, reslen, reserr)
ps = pd - 1; /* | pi | pc | v j */
/* |---------| */
lseq = pseq->seqlen;
lpat = ppat->patlen;
sseq = pseq->data - 1;
amask = ONEMASK >> lpat;
//amask = ONEMASK >> lpat;
amask = 0x1L << (ppat->patlen);
for (j = 0 ; j <= lpat ; j++) {
for (i = 0 , px = sseq ; i <= lseq ; i++, px++) {
if (i && j) {
dindel = MIN(*pi, *pd) + 1;
if (j == lpat) dindel--;
dsub = *ps + KRONECK(ppat->smat[*px], amask);
// fprintf(stderr, "mismatch : %d %d %d %d\n",j,*px,KRONECK(ppat->smat[*px], amask),amask);
*pc = MIN(dindel, dsub);
}
else if (i) /* j == 0 */
*pc = *pi + 1;
else if (j) /* i == 0 */
*pc = *pd + 1;
*pc = *pd;
else /* root */
*pc = 0;
fprintf(stderr," %02d",*pc);
pc++;
pi++;
pd++;
ps++;
}
fprintf(stderr,"\n");
amask <<= 1;
// amask <<= 1;
amask >>= 1;
}
pc--;
@@ -331,6 +340,7 @@ int32_t NwsPatAlign(pseq, ppat, nerr, reslen, reserr)
*reserr++ = *pc;
npos++;
}
fprintf(stderr,"i=%d *pc = %d<%d, reserr = %d npos = %d\n",i,*pc,nerr,*(reserr-1),npos);
}
return npos;