diff --git a/src/ecoprimer.c b/src/ecoprimer.c index 71220ab..88662bf 100644 --- a/src/ecoprimer.c +++ b/src/ecoprimer.c @@ -134,9 +134,9 @@ void initoptions(poptions_t options) options->refseq=NULL; options->circular=0; options->doublestrand=1; - options->strict_quorum=0.3; + options->strict_quorum=0.7; options->strict_exclude_quorum=0.1; - options->sensitivity_quorum=0.3; + options->sensitivity_quorum=0.9; options->false_positive_quorum=0.1; options->strict_three_prime=0; options->r=0; diff --git a/src/libecoprimer/pairs.c b/src/libecoprimer/pairs.c index 08e3ac4..ecb302b 100644 --- a/src/libecoprimer/pairs.c +++ b/src/libecoprimer/pairs.c @@ -252,11 +252,16 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid, { // For all primers matching the sequence - for(j=i+1; - (jprimer_length) < options->lmax); - j++ - ) + //for(j=i+1; + // (jprimer_length) < options->lmax); + // j++ + // ) + for (j=i+1; jprimer_length) continue; + distance = matches[j].position - matches[i].position - options->primer_length; + if (distance >= options->lmax) break; // For all not too far primers @@ -448,6 +453,7 @@ static void buildPrimerPairsForOneSeq(uint32_t seqid, // } + } } } diff --git a/src/libecoprimer/taxstats.c b/src/libecoprimer/taxstats.c index d1ca219..5b2d64e 100644 --- a/src/libecoprimer/taxstats.c +++ b/src/libecoprimer/taxstats.c @@ -175,8 +175,10 @@ static int cmpamp(const void *ampf1, const void* ampf2) void twalkaction (const void *node, VISIT order, int level) { - const size_t taxid=(size_t)node; - counttaxon(taxid); + int32_t *taxid = (int32_t*)node; + //const size_t taxid=(size_t)node; + //printf ("\t%d:%p, ", *taxid, node); + counttaxon(*taxid); } int32_t gtxid;