obitools/ecoprimers
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 2 Wiki Activity

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/branches/eric-test@185 60f365c0-8329-0410-b2a4-ec073aeeaa1d

Browse Source
This commit is contained in:
Eric Coissac
2009-03-10 08:49:11 +00:00
parent dffebd5826
commit d911d6bd20
5 changed files with 19 additions and 12 deletions
Download Patch File Download Diff File Expand all files Collapse all files

BIN
src/ecoPrimer
View File

Binary file not shown.

2
src/global.mk
View File

@ -3,7 +3,7 @@ LIBPATH= -Llibapat -LlibecoPCR -Llibecoprimer
MAKEDEPEND = gcc -D$(MACHINE) -M $(CPPFLAGS) -o $*.d $<
CC=gcc
CFLAGS= -W -Wall -O3 -m64 -fast -g
CFLAGS= -W -Wall -O5 -m64 -fast -g
#CFLAGS= -W -Wall -O0 -m64 -g
#CFLAGS= -W -Wall -O5 -fast -g

4
src/libecoprimer/aproxpattern.c
View File

@ -61,7 +61,7 @@ void encodeSequence(ecoseq_t *seq)
for (i=0;i<seq->SQ_length;i++,data++,cseq++)
{
*data = encoder[(IS_UPPER(*cseq) ? *cseq - 'A' : 'Z')];
*data = encoder[(IS_UPPER(*cseq) ? *cseq : 'Z') - 'A'];
}
}
@ -82,7 +82,7 @@ pprimercount_t lookforAproxPrimer(pecodnadb_t database, uint32_t seqdbsize,uint3
uint32_t inSequenceQuorum;
uint32_t outSequenceQuorum;
bool_t conserved = TRUE;
//poslist_t ttt;

18
src/libecoprimer/pairs.c
View File

@ -275,6 +275,7 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
pprimer_t wswp;
bool_t bswp;
size_t distance;
bool_t strand;
for (i=0;i < primers->size; i++)
{
@ -362,7 +363,8 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
// Standardize the pair
if (current.p2->word < current.p1->word)
strand = current.p2->word > current.p1->word;
if (!strand)
{
wswp = current.p1;
current.p1=current.p2;
@ -384,7 +386,7 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
pcurrent->inexample++;
pcurrent->sumd+=distance;
if (pcurrent->maxd=DMAX || distance > pcurrent->maxd)
if ((pcurrent->maxd==DMAX) || (distance > pcurrent->maxd))
pcurrent->maxd = distance;
if (distance < pcurrent->mind)
@ -412,10 +414,14 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
}
}
pcurrent->pcr.amplifias[pcr.ampcount].length=distance;
pcurrent->pcr.amplifias[pcr.ampcount].sequence=*(seqdb[seqid]);
// pcurrent->pcr.amplifias[pcr.ampcount].strand= ;
// pcurrent->pcr.amplifias[pcr.ampcount].amplifia= ;
pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].length=distance;
pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].sequence=seqdb[seqid];
pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].strand=strand;
if (strand)
pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].amplifia= seqdb[seqid]->SQ + matches[i].position + options->primer_length;
else
pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].amplifia= seqdb[seqid]->SQ + matches[j].position - 1 ;
pcurrent->pcr.ampcount++;

7
src/libecoprimer/pairtree.c
View File

@ -39,6 +39,7 @@ static ppairlist_t newpairlist(ppairlist_t parent, size_t size)
if (parent)
parent->next=(void*)tmp;
return tmp;
}
@ -103,7 +104,7 @@ ppair_t insertpair(pair_t key,
if (list->last->paircount==list->last->pairslots)
{
list->last->next=newpairlist(list,100);
list->last->next=newpairlist(list->last,100);
list->last=list->last->next;
}
@ -121,13 +122,13 @@ ppair_t insertpair(pair_t key,
ppairtree_t initpairtree(ppairtree_t tree)
{
fprintf(stderr,"coucou from initpairtree\n");
if (!tree)
tree = ECOMALLOC(sizeof(pairtree_t),"Cannot allocate pair tree");
tree->first=newpairlist(NULL,500);
tree->first=newpairlist(NULL,300);
tree->last=tree->first;
tree->tree=NULL;
return tree;
}