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Sequence circularity, bug correction

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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@167 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Eric Coissac
2008-04-28 16:46:18 +00:00
parent d863b7e48e
commit 708b7c387e
5 changed files with 18 additions and 13 deletions
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6
src/ecopcr.c
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@ -239,7 +239,7 @@ void printRepeat(ecoseq_t *seq,
error1, error1,
oligo2, oligo2,
error2, error2,
amplength, amplength - o1->patlen - o2->patlen,
amplifia, amplifia,
seq->DE seq->DE
); );
@ -387,9 +387,11 @@ int main(int argc, char **argv)
strcpy(oligo2,argv[optind]); strcpy(oligo2,argv[optind]);
if (circular) if (circular)
{
circular = strlen(oligo1); circular = strlen(oligo1);
if (strlen(oligo2)>(size_t)circular) if (strlen(oligo2)>(size_t)circular)
circular = strlen(oligo2); circular = strlen(oligo2);
}
} }
else else
errflag++; errflag++;
@ -499,7 +501,7 @@ int main(int argc, char **argv)
for (i=0; i < o1Hits;i++) for (i=0; i < o1Hits;i++)
{ {
posi = apatseq->hitpos[0]->val[i]; posi = apatseq->hitpos[0]->val[i];
if (posi < apatseq->seqlen) if (posi < apatseq->seqlen)
{ {
erri = apatseq->hiterr[0]->val[i]; erri = apatseq->hiterr[0]->val[i];

3
src/libapat/Makefile
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@ -9,6 +9,7 @@ SRCS=$(SOURCES)
OBJECTS= $(patsubst %.c,%.o,$(SOURCES)) OBJECTS= $(patsubst %.c,%.o,$(SOURCES))
LIBFILE= libapat.a LIBFILE= libapat.a
RANLIB=ranlib
include ../global.mk include ../global.mk
@ -20,4 +21,4 @@ clean:
$(LIBFILE): $(OBJECTS) $(LIBFILE): $(OBJECTS)
ar -cr $@ $? ar -cr $@ $?
$(RANLIB) $@

12
src/libapat/apat_search.c
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@ -80,14 +80,14 @@ int CreateS(Pattern *ppat, Int32 lalpha)
/* -------------------------------------------- */ /* -------------------------------------------- */
Int32 ManberNoErr(Seq *pseq, Pattern *ppat, int patnum,int begin,int length) Int32 ManberNoErr(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
{ {
Int32 pos; UInt32 pos;
UInt32 smask, r; UInt32 smask, r;
UInt8 *data; UInt8 *data;
StackiPtr *stkpos, *stkerr; StackiPtr *stkpos, *stkerr;
UInt32 end; UInt32 end;
end = begin + length; end = begin + length;
end = (end <= pseq->seqlen) ? end:pseq->seqlen; end = (end <= (size_t)(pseq->seqlen+pseq->circular)) ? end:(size_t)(pseq->seqlen+pseq->circular);
/* create local masks */ /* create local masks */
@ -127,7 +127,7 @@ Int32 ManberNoErr(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
Int32 ManberSub(Seq *pseq, Pattern *ppat, int patnum,int begin,int length) Int32 ManberSub(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
{ {
int e, emax, found; int e, emax, found;
Int32 pos; UInt32 pos;
UInt32 smask, cmask, sindx; UInt32 smask, cmask, sindx;
UInt32 *pr, r[2 * MAX_PAT_ERR + 2]; UInt32 *pr, r[2 * MAX_PAT_ERR + 2];
UInt8 *data; UInt8 *data;
@ -135,7 +135,7 @@ Int32 ManberSub(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
UInt32 end; UInt32 end;
end = begin + length; end = begin + length;
end = (end <= pseq->seqlen) ? end:pseq->seqlen; end = (end <= (size_t)(pseq->seqlen+pseq->circular)) ? end:(size_t)(pseq->seqlen+pseq->circular);
/* create local masks */ /* create local masks */
emax = ppat->maxerr; emax = ppat->maxerr;
@ -193,7 +193,7 @@ Int32 ManberSub(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
Int32 ManberIndel(Seq *pseq, Pattern *ppat, int patnum,int begin,int length) Int32 ManberIndel(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
{ {
int e, emax, found; int e, emax, found;
Int32 pos; UInt32 pos;
UInt32 smask, cmask, sindx; UInt32 smask, cmask, sindx;
UInt32 *pr, r[2 * MAX_PAT_ERR + 2]; UInt32 *pr, r[2 * MAX_PAT_ERR + 2];
UInt8 *data; UInt8 *data;
@ -201,7 +201,7 @@ Int32 ManberIndel(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
UInt32 end; UInt32 end;
end = begin + length; end = begin + length;
end = (end <= pseq->seqlen) ? end:pseq->seqlen; end = (end <= (size_t)(pseq->seqlen+pseq->circular)) ? end:(size_t)(pseq->seqlen+pseq->circular);
/* create local masks */ /* create local masks */
emax = ppat->maxerr; emax = ppat->maxerr;

2
src/libecoPCR/Makefile
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@ -15,6 +15,7 @@ SRCS=$(SOURCES)
OBJECTS= $(patsubst %.c,%.o,$(SOURCES)) OBJECTS= $(patsubst %.c,%.o,$(SOURCES))
LIBFILE= libecoPCR.a LIBFILE= libecoPCR.a
RANLIB= ranlib
include ../global.mk include ../global.mk
@ -27,3 +28,4 @@ clean:
$(LIBFILE): $(OBJECTS) $(LIBFILE): $(OBJECTS)
ar -cr $@ $? ar -cr $@ $?
$(RANLIB) $@

8
src/libecoPCR/ecoapat.c
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@ -50,13 +50,13 @@ void EncodeSequence(SeqPtr seq)
while (*cseq) { while (*cseq) {
*data++ = (IS_UPPER(*cseq) ? *cseq - 'A' : 0x0); *data = (IS_UPPER(*cseq) ? *cseq - 'A' : 0x0);
data++;
cseq++; cseq++;
} }
for (i=0,cseq=seq->cseq;i < seq->circular; i++,cseq++) for (i=0,cseq=seq->cseq;i < seq->circular; i++,cseq++,data++)
*data++ = (IS_UPPER(*cseq) ? *cseq - 'A' : 0x0); *data = (IS_UPPER(*cseq) ? *cseq - 'A' : 0x0);
for (i = 0 ; i < MAX_PATTERN ; i++) for (i = 0 ; i < MAX_PATTERN ; i++)
seq->hitpos[i]->top = seq->hiterr[i]->top = 0; seq->hitpos[i]->top = seq->hiterr[i]->top = 0;