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fixed specificity and pairing bugs

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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@287 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Eric Coissac
2010-11-29 22:57:56 +00:00
parent dd08d73dda
commit ca1e9d8899
3 changed files with 17 additions and 9 deletions
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4
src/ecoprimer.c
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@ -134,9 +134,9 @@ void initoptions(poptions_t options)
options->refseq=NULL; options->refseq=NULL;
options->circular=0; options->circular=0;
options->doublestrand=1; options->doublestrand=1;
options->strict_quorum=0.3; options->strict_quorum=0.7;
options->strict_exclude_quorum=0.1; options->strict_exclude_quorum=0.1;
options->sensitivity_quorum=0.3; options->sensitivity_quorum=0.9;
options->false_positive_quorum=0.1; options->false_positive_quorum=0.1;
options->strict_three_prime=0; options->strict_three_prime=0;
options->r=0; options->r=0;

16
src/libecoprimer/pairs.c
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@ -252,11 +252,16 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
{ {
// For all primers matching the sequence // For all primers matching the sequence
for(j=i+1; //for(j=i+1;
(j<matchcount) // (j<matchcount)
&& ((distance=matches[j].position - matches[i].position - options->primer_length) < options->lmax); // && ((distance=matches[j].position - matches[i].position - options->primer_length) < options->lmax);
j++ // j++
) // )
for (j=i+1; j<matchcount; j++)
{
if (matches[j].position - matches[i].position <= options->primer_length) continue;
distance = matches[j].position - matches[i].position - options->primer_length;
if (distance >= options->lmax) break;
// For all not too far primers // For all not too far primers
@ -448,6 +453,7 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid,
// //
} }
}
} }
} }

6
src/libecoprimer/taxstats.c
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@ -175,8 +175,10 @@ static int cmpamp(const void *ampf1, const void* ampf2)
void twalkaction (const void *node, VISIT order, int level) void twalkaction (const void *node, VISIT order, int level)
{ {
const size_t taxid=(size_t)node; int32_t *taxid = (int32_t*)node;
counttaxon(taxid); //const size_t taxid=(size_t)node;
//printf ("\t%d:%p, ", *taxid, node);
counttaxon(*taxid);
} }
int32_t gtxid; int32_t gtxid;