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New option for reference sequence

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and bug correction for insequence count

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@218 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Eric Coissac
2009-06-23 14:11:39 +00:00
parent 40644bc85f
commit 3a617890ca
5 changed files with 123 additions and 38 deletions
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42
src/libecoprimer/pairs.c
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@ -205,8 +205,8 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
{
if (primers->primers[i].directCount[seqid]==1)
{
matches[j].primer = primers->primers+i;
matches[j].strand=TRUE;
matches[j].primer = primers->primers+i;
matches[j].strand=TRUE;
matches[j].position=primers->primers[i].directPos[seqid].value;
j++;
}
@ -222,8 +222,8 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
{
if (primers->primers[i].reverseCount[seqid]==1)
{
matches[j].primer = primers->primers+i;
matches[j].strand=FALSE;
matches[j].primer = primers->primers+i;
matches[j].strand=FALSE;
matches[j].position=primers->primers[i].reversePos[seqid].value;
j++;
}
@ -270,6 +270,8 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
current.sumd=0;
current.inexample=0;
current.outexample=0;
current.curseqid = 0;
current.refsequence=-1;
// Standardize the pair
@ -285,7 +287,7 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
current.asdirect1=current.asdirect2;
current.asdirect2=bswp;
}
// Look for the new pair in already seen pairs
@ -295,7 +297,7 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
if (seqdb[seqid]->isexample)
{
pcurrent->inexample++;
//pcurrent->inexample++;
pcurrent->sumd+=distance;
if ((pcurrent->maxd==DMAX) || (distance > pcurrent->maxd))
@ -304,11 +306,29 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
if (distance < pcurrent->mind)
pcurrent->mind = distance;
}
else
pcurrent->outexample++;
//else
// pcurrent->outexample++;
if ((pcurrent->outexample+pcurrent->inexample)==1)
if (pcurrent->curseqid != (seqid+1))
{
if (seqdb[seqid]->isexample)
pcurrent->inexample++;
else
pcurrent->outexample++;
if (pcurrent->curseqid != 0)
pcurrent->curseqid = seqid+1;
}
/*if ((pcurrent->outexample+pcurrent->inexample)==0)
{
fprintf(stderr,"pcurrent->outexample+pcurrent->inexample=0!\n");
exit(0);
}*/
if (pcurrent->curseqid == 0)//((pcurrent->outexample+pcurrent->inexample)==1)
{
pcurrent->curseqid = seqid+1;
paircount++;
pcurrent->pcr.ampslot=200;
pcurrent->pcr.ampcount=0;
@ -326,9 +346,13 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
}
}
if (seqid==options->refseqid)
pcurrent->refsequence=seqid;
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;
pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].begin=matches[i].position + options->primer_length;
pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].end= matches[j].position - 1;
if (strand)
pcurrent->pcr.amplifias[pcurrent->pcr.ampcount].amplifia= seqdb[seqid]->SQ + matches[i].position + options->primer_length;